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Rupert, David

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Feb 11, 2015, 12:28:26 PM2/11/15

to gen...@soe.ucsc.edu, Hasi, Minire, Cody, Jannine D

I have 2 text files for Chromosome 18 p- work and want to color code each gene track with 1 of 5 colors and set it to “Pack”. The info pages show that with pack you get the option for a range of greys or blues or browns only

Text file “hg19-p-_pack” has the upper section colored as we want, but, keeping the coloring, can we display it like the below section, the more compact format?

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr18%3A1-17176994&hgsid=411456277_Sc7n6zdsTmmJQvpPO50peNKF7IQc

Text file “hg19-p-_pack2_test” uses the pack layout but only shows grey.

http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr18%3A1-17307123&hgsid=411456493_nOuzCdGDFJlXalL68NS4Mi64fDSO

David C. Rupert

MED 540F.1

O-210-567-5251

C- 210-452-6536

"Happiness equals reality minus expectations" Tom Magliozzi

From: gen...@soe.ucsc.edu [mailto:gen...@soe.ucsc.edu]
Sent: Wednesday, February 11, 2015 11:12 AM
To: Digest recipients
Subject: [genome] Digest for gen...@soe.ucsc.edu - 9 updates in 7 topics

gen...@soe.ucsc.edu

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Topic digest
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· dbsnp of MAF less than 1 percentage - 1 Update

· downloading a table with cell line information - 3 Updates

· reciprocal best hit - 1 Update

· registering a track hub with UCSC - 1 Update

· genome browser - 1 Update

· Variant Annotation Integrator - phyloP100 issue - 1 Update

· Digest for gen...@soe.ucsc.edu - 11 updates in 6 topics - 1 Update

dbsnp of MAF less than 1 percentage

Matthew Speir <msp...@soe.ucsc.edu>: Feb 10 02:42PM -0800

Hi Alva,

I'm assuming that you are downloading your "snp141Common" data from the
Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19, or from
our download server, http://hgdownload.soe.ucsc.edu/downloads.html. To
get SNP data for hg19 from the Table Browser, just ensure that have
selected hg19 from the "assembly" drop-down menu on the Table Browser.
If you are downloading SNP data from our downloads server, you should
see "hg19" in the URL like so
http://hgdownload.soe.ucsc.edu/goldenPath/*hg19*/database/snp141Common.txt.gz.

Please also note that some alleles, such as rs376643643, have no
frequency data reported at all. The alleleNs and alleleFreqs, or 24th
and 25th columns, will be empty if there are no frequency data
available. For example, you can see the alleleNs and alleleFreqs columns
from the rs376643643 entry in snp141 are empty:

+-------------+----------+-------------+
| name | alleleNs | alleleFreqs |
+-------------+----------+-------------+
| rs376643643 | | |
+-------------+----------+-------------+

I hope this is helpful. If you have any further questions, please reply
to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

On 2/6/15 3:54 AM, Rani James, Alva wrote:

downloading a table with cell line information

Eric Foss <ef...@fredhutch.org>: Feb 10 01:02PM -0800

Dear UCSC Genome Browser,

You have a page with information about many cell lines here:

http://genome.ucsc.edu/ENCODE/cellTypes.html <http://genome.ucsc.edu/ENCODE/cellTypes.html>

Can I download this as a table?

Thank you.

Eric

Brian Lee <bria...@soe.ucsc.edu>: Feb 10 01:56PM -0800

Dear Eric,

Thank you for using the UCSC Genome Browser and your question about the
cell lines listed on the ENCODE Cell Types 2007 - 2012 page:
http://genome.ucsc.edu/ENCODE/cellTypes.html

Please note that the ENCODE data at UCSC is currently limited to the span
up until 2012. For current ENCODE project release information, please see
the ENCODE portal:
https://www.encodeproject.org/help/getting-started

For the data at UCSC, the metadata about antibodies, cell types, labs,
protocols, treatments, ect. was collected into a controlled vocabulary
document. That "cv.ra" document can be found on the ENCODE Downloads page,
http://genome.ucsc.edu/ENCODE/downloads.html, under at "Metadata" section.
Here is the link: http://hgdownload.cse.ucsc.edu/goldenPath/encodeDCC/cv.ra

When opening the cv.ra text file, you will see it is a collection of
stanza, of different types for each kind of metadata (antibodies, cell
types, labs, protocols,). The first section of the file is the collection
of information about the "type Cell Line", where there are terms and tags,
such as GM12878 or BC_Placenta_UHN00189. The term is used to open CGI
links:
http://genome.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&deprecated=true&term=GM12878

You may find this UCSC ENCODE resource page helpful,
http://genome.ucsc.edu/ENCODE/FAQ/, where you can find some FAQs and links
to the "Experiment Matrix" which profiles Cell Lines against Assay Types
(for both mouse and human). There is also the ChIP-seq Matrix available,
which visualizes Cell Lines agains Antibody:
http://genome.ucsc.edu/ENCODE/dataMatrix/encodeChipMatrixHuman.html

Also, every ENCODE file has a line about that file's metadata in a
files.txt file located in the related downloads page. See this FAQ, and the
one above it, for more information:
http://genome.ucsc.edu/ENCODE/FAQ/#release7

There are also metaData tables for the mm9 and hg19 databases, linking
every file to it's metadata. If you are interested in using MySQL, please
see this resource: http://genome.ucsc.edu/goldenPath/help/mysql.html The
following command would go through the metaData table for hg19 and pull the
distinct related cell lines: mysql --user=genome --host=
genome-mysql.cse.ucsc.edu -A -Ne 'select distinct val from metaDb where var
like "cell";' hg19

That list, which would include terms like, GM12878 and
BC_Placenta_UHN00189, could be put into the CGI link for hgEncodeVocab, or
searched in the cv.ra to find more information.

Thank you again for your inquiry and using the UCSC Genome Browser. If you
have any further questions, please reply to gen...@soe.ucsc.edu. All
messages sent to that address are archived on a publicly-accessible forum.
If your question includes sensitive data, you may send it instead to
genom...@soe.ucsc.edu.

All the best,

Brian Lee
UCSC Genome Bioinformatics Group

Brian Lee <bria...@soe.ucsc.edu>: Feb 10 02:08PM -0800

Dear Eric,

In case it might be of interest, I forgot to add that you can add several
cv.ra terms to the hgEncodeVocab CGI.

Below are two links, one for hg19 and one for mm9, where all the distinct
cell terms from the related metadata tables have been put into a URL, each
with a comma (term=X,Y,Z) providing a type of table seen on the cellTypes
page:
mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -Ne 'select
distinct val from metaDb where var like "cell";' hg19

http://genome.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&deprecated=true&term=8988T,A549,Adult_CD4_Th0,Adult_CD4_Th1,AG04449,AG04450,AG09309,AG09319,AG10803,AoAF,AoSMC,Astrocy,BC_Adrenal_Gland_H12803N,BC_Brain_H11058N,BC_Breast_02-03015,BC_Jejunum_H12817N,BC_Kidney_01-11002,BC_Left_Ventricle_N41,BC_Leukocyte_UHN00204,BC_Liver_01-11002,BC_Lung_01-11002,BC_Pancreas_H12817N,BC_ Pericardium_H12529N,BC_Placenta_UHN00189,BC_Skeletal_Muscle_01-11002,BC_Skeletal_Muscle_H12817N,BC_Skin_01-11002,BC_Small_Intestine_01-11002,BC_Stomach_01-11002,BC_Testis_N30,BC_Uterus_BN0765,BE2_C,BG02ES,BJ,bone_marrow_HS27a,bone_marrow_HS5,bone_marrow_MSC,Caco-2,CD20+,CD20+_RO01778,CD20+_RO01794,CD34+_Mobilized,CD4+_Naive_Wb11970640,CD4+_Naive_Wb78495824,Cerebellum_OC,Cerebrum_frontal_OC,Chorion,CLL,CMK,Colo829,Colon_OC,Dnd41,ECC-1,Endometrium_OC,Fibrobl,Fibrobl_GM03348,FibroP,FibroP_AG08395,FibroP_AG08396,FibroP_AG20443,Frontal_cortex_OC,GC_B_cell,Gliobla,GM04503,GM04504,GM06990,GM08714,GM10248,GM10266,GM10847,GM12801,GM12812,GM12813,GM12864,GM12865,GM12866,GM12867,GM12868,GM12869,GM12870,GM12871,GM12872,GM12873,GM12874,GM12875,GM12878,GM12878-XiMat,GM12891,GM12892,GM13976,GM13977,GM15510,GM18505,GM18507,GM18526,GM18951,GM19099,GM19193,GM19238,GM19239,GM19240,GM20000,H1-hESC,H1-neurons,H7-hESC,H9ES,HA-h,HA-sp,HAc,HAEpiC,HAoAF,HAoEC,HBMEC,HBVP,HBVSMC,HCF,HCFaa,HCH,HCM,HConF,HCPEpiC, HCT-116,Heart_OC,HEEpiC,HEK293,HEK293-T-REx,HEK293T,HeLa-S3,Hepatocytes,HepG2,HFDPC,HFF,HFF-Myc,HGF,HIPEpiC,HL-60,HMEC,HMEpC,HMF,hMNC-CB,hMNC-PB,hMSC-AT,hMSC-BM,hMSC-UC,HMVEC-dAd,HMVEC-dBl-Ad,HMVEC-dBl-Neo,HMVEC-dLy-Ad,HMVEC-dLy-Neo,HMVEC-dNeo,HMVEC-LBl,HMVEC-LLy,HNPCEpiC,HOB,HPAEC,HPAEpiC,HPAF,HPC-PL,HPDE6-E6E7,HPdLF,HPF,HPIEpC,HRCEpiC,HRE,HRGEC,HRPEpiC,HSaVEC,HSMM,HSMMtube,HSMMtube_FSHD,HSMM_emb,HSMM_FSHD,HT-1080,HTR8svn,Huh-7,Huh-7.5,HUVEC,HVMF,HWP,IMR90,iPS,iPS_CWRU1,iPS_hFib2_iPS4,iPS_hFib2_iPS5,iPS_NIHi11,iPS_NIHi7,Ishikawa,Jurkat,K562,Kidney_OC,LHCN-M2,LNCaP,Lung_OC,M059J,MCF-7,MCF10A-Er-Src,Medullo,Medullo_D341,Melano,Mel_2183,Monocytes-CD14+,Monocytes-CD14+_RO01746,MRT_A204,MRT_G401,MRT_TTC549,Myometr,Naive_B_cell,NB4,NH-A,NHBE,NHBE_RA,NHDF,NHDF-Ad,NHDF-neo,NHEK,NHEM.f_M2,NHEM_M2,NHLF,None,NT2-D1,Olf_neurosphere,Osteobl,ovcar-3,PANC-1,Pancreas_OC,PanIsletD,PanIslets,PBDE,PBDEFetal,PBMC,PFSK-1,pHTE,PrEC,ProgFib,prostate,Psoas_muscle_OC,Raji,RCC_7860,RPMI-7951,RPTEC,RWPE1,SAEC, SH-SY5Y,SK-N-MC,SK-N-SH,SK-N-SH_RA,SKMC,Small_intestine_OC,Spleen_OC,Stellate,T-47D,Th1,Th17,Th1_Wb33676984,Th1_Wb54553204,Th2,Th2_Wb33676984,Th2_Wb54553204,Treg_Wb78495824,Treg_Wb83319432,U2OS,U87,UCH-1,Urothelia,WERI-Rb-1,WI-38

mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -Ne 'select
distinct val from metaDb where var like "cell";' mm9

http://genome.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&deprecated=true&term=10T1/2,3134,416B,A20,Adrenal,B-cell_(CD19+),B-cell_(CD43-),BAT,Bladder,BMDM,B oneMarrow,C2C12,Cerebellum,Cerebrum,CH12,CNS,Colon,Cortex,Duodenum,EPC_(CD117+_CD71+_TER119+),EPC_(CD117+_CD71+_TER119-),EPC_(CD117+_CD71-_TER119-),EPC_(CD117-_CD71+_TER119+),EpiSC-5,EpiSC-7,Erythrobl,ES-46C,ES-Bruce4,ES-CJ7,ES-D3,ES-E14,ES-EM5Sox17huCD25,ES-TT2,ES-WW6,ES-WW6_F1KO,FatPad,Fibroblast,ForelimbBud,FrontalLobe,FVLstem,FVprogenitor,G1E,G1E-ER4,GenitalFatPad,HeadlessEmbryo,Heart,HindlimbBud,J185a,Kidney,L1210,LgIntestine,Limb,Liver,Lung,MammaryGland,MEF,Megakaryo,MEL,MEP,Mesoderm,mG/ER,NIH-3T3,OlfactBulb,Ovary,Patski,Placenta,Retina,SkMuscle,SmIntestine,Spleen,Stomach,SubcFatPad,T-Naive,Testis,THelper-Activated,Thymus,TReg,TReg-Activated,WholeBrain,ZhBTc4

Thank you again for your inquiry and using the UCSC Genome Browser. If you
have any further questions, please reply to gen...@soe.ucsc.edu. All
messages sent to that address are archived on a publicly-accessible forum.
If your question includes sensitive data, you may send it instead to
genom...@soe.ucsc.edu.

All the best,
Brian Lee

reciprocal best hit

"Steve Heitner" <st...@soe.ucsc.edu>: Feb 10 01:46PM -0800

Hello, Anaïs.

You should indeed get single coverage. Please ensure that you are following the exact procedure. The warning message is probably an indication of where the problem is occurring.

Please contact us again at gen...@soe.ucsc.edu if you have any further questions. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

---
Steve Heitner
UCSC Genome Bioinformatics Group

From: Anaïs Gouin [mailto:anais...@irisa.fr]
Sent: Monday, February 09, 2015 6:26 AM
To: gen...@soe.ucsc.edu
Subject: Re: [genome] reciprocal best hit

A last question to finish. I thought that getting the reciprocal best chains would give me only one2one regions.
By one2one I mean that a region in the first genome match only with one other region of the second genome.

But actually here is an example of my reciprocal best pipeline :

chain 237344 scaffold_1 873266 + 56 5232 SFRU_RICE_003848 4548 - 1112 4548 24274
chain 5577 scaffold_1 873266 + 233 5622 SFRU_RICE_003530 4082 - 731 3943 31497

Then I have two chains from the same region in scaffold_1 that matches with two defferent scaffolds of my second genome.

Can you give me some explanations about the reciprocal best chains please?

Thanks a lot in advance,

Anaïs

_____

De: "Anaïs Gouin" <anais...@irisa.fr>
À: gen...@soe.ucsc.edu
Envoyé: Lundi 9 Février 2015 12:53:00
Objet: Re: [genome] reciprocal best hit

Thank you very much for your answer and for the link, it was indeed very useful.

I have however a little question. I got no error messages during all steps of reciprocal best. But I get the warnings at the end :

Warning: mais rbest net coverage 238772284 != riz 238772322

Warning: mais rbest chain coverage 238772322 != net cov 238772284

Is it a problem? Or Does not it come from the fact that the chains can cover a longer region in the ref than in the query or reciprocally (because of gaps)?

Thanks again,

Anaïs

_____

De: "Matthew Speir" <msp...@soe.ucsc.edu>
À: "Anaïs Gouin" <anais...@irisa.fr>, gen...@soe.ucsc.edu
Envoyé: Vendredi 6 Février 2015 23:24:50
Objet: Re: [genome] reciprocal best hit

Hi Anaïs,

Thank you for your question about . You can look at the following GenomeWiki page for some sample scripts that you can use to create your own Reciprocal Best or Syntenic Net file: http://genomewiki.ucsc.edu/index.php/HowTo:_Syntenic_Net_or_Reciprocal_Best. You should be able to find any of the utilities referenced in those scripts on our download server at http://hgdownload.soe.ucsc.edu/downloads.html under the appropriate folder for your machine.

If you are ever curious about what a particular UCSC Genome Browser utility does, you can always run it on the command line without any arguments to see that usage message. For example, if you run chainStichId without any arguments, you should see the following usage message:

chainStitchId - Join chain fragments with the same chain ID into a single
chain per ID. Chain fragments must be from same original chain but
must not overlap. Chain fragment scores are summed.
usage:
chainStitchId in.chain out.chain

I hope this is helpful. If you have any further questions, please reply to gen...@soe.ucsc.edu. All messages sent to that address are archived on a publicly-accessible Google Groups forum. If your question includes sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

On 2/5/15 9:00 AM, Anaïs Gouin wrote:

Hello,

I runned lastz + axtchain to do a whole genome comparison between two variants of a same insect, that are almost considered as two different species. I would like tu run the netting step, following the comments here :

http://genomewiki.ucsc.edu/index.php/Whole_genome_alignment_howto

However, I also heard about the reciprocal best analysis, but I do not find example to follow. I found this post on the UCSC genome support forum

http://redmine.soe.ucsc.edu/forum/index.php?t=msg <http://redmine.soe.ucsc.edu/forum/index.php?t=msg&goto=10873&S=4a5e82e0a351417ce9833560af5663e2> &goto=10873&S=4a5e82e0a351417ce9833560af5663e2

so I was tempted to use the chainStitchId/chainSwap program but I am not sure of what to do first.

In the example I found they applied chainStitchId/chainSwap/chainSort over the set of best chains (mm9.hg19.tBest.chain) before netting. Is there a specific program I do not hear about selecting the best chains, or is it chainPreNet that does this thing (+ the netting that allows the target positions to be single coverage)?

Here is what I would from what I read knowing that

Lastz+axtchain with A genome as reference and B genome as query

chainSort/chainPreNet/chainNet/netSyntenic do get the netting of the chains

extraction of chains from nets (ref-referenced)

chainStitchId/chainSwap to get the chains query-reference

chainSort/chainPreNet/chainNet/netSyntenic to get reciprocal best nets

netChainSubset/chainStitchId to extract again of reciprocal best chains

chainSwap to swa agin to get the reciprocal best chains in target reference (A genome)

and netting again to finish.

Do I do it in the good way? Can you give some explanations about chainStitchId? I am not sure to well understand what it does.

Thank you very much in advance for your help,

Anaïs

--

--

registering a track hub with UCSC

Matthew Speir <msp...@soe.ucsc.edu>: Feb 10 12:19PM -0800

Hi LaDeana,

Thank you for making this data available! I will be the QA engineer
tasked with reviewing your assembly hub and later adding it to the list
of publicly available hubs. If you haven't already, you may also find it
helpful to read our list of track hub guidelines at
http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines. It contains
a list of common suggestions and requests that we make of hub providers
before adding their data to the list. At minimum, we request that each
track have a description page with contact information (usually an email
address). Feel free to send us additional questions should you have them
as you work through those guidelines. I will also review your hub and
send along some suggested improvements.

I hope this is helpful. If you have any further questions, please reply
to gen...@soe.ucsc.edu. All messages sent to that address are archived
on a publicly-accessible Google Groups forum. If your question includes
sensitive data, you may send it instead to genom...@soe.ucsc.edu.

Matthew Speir
UCSC Genome Bioinformatics Group

On 2/7/15 8:57 PM, LaDeana Hillier wrote:

genome browser

Daria Merkurjev <dashame...@gmail.com>: Feb 10 11:11AM -0800

Thank you very much for your help!

Daria.

On Tue, Feb 10, 2015 at 7:22 AM, Enrique Medina-Acosta <

Variant Annotation Integrator - phyloP100 issue

"Steve Heitner" <st...@soe.ucsc.edu>: Feb 10 11:08AM -0800

Hello, Paolo.

This is the result of the way the VAI is specifically expecting the file to be sorted. Currently, it expects to see:

chr1
chr10
chr11
chr12
chr13
chr14
chr15
chr16
chr17
chr18
chr19
chr2
chr20
chr21
chr22
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chrX
chrY

We will work on relaxing the sorting expectations, but in the meantime, you can sort your VCF file with the following and try again:

sort -k1,1 -k 2n,2n my.vcf > my.ucsc.vcf

Please contact us again at gen...@soe.ucsc.edu if you have any further questions. Questions sent to that address will be archived in a publicly-accessible forum for the benefit of other users. If your question contains sensitive data, you may send it instead to genom...@soe.ucsc.edu.

---
Steve Heitner
UCSC Genome Bioinformatics Group

-----Original Message-----
From: Paolo Uva [mailto:paol...@crs4.it]
Sent: Monday, February 09, 2015 8:12 AM
To: gen...@soe.ucsc.edu
Subject: [genome] Variant Annotation Integrator - phyloP100 issue

Dear UCSC staff,

I'm encountering a a problem with Variant Annotation Integrator.

I uploaded successfully as a custom track a VCF with 7,000 lines, with variants sorted as chr1...chr9,chr10...chr22, chrX, chrY.

I submit to VAI, selecting just '100 vertebrates Basewise Conservation by PhyloP'.
In the "Select Genes" section, I selected 'UCSC genes' (default).

VAI runs and produces a file with variants from chr1 to chr9 only.
The last line contains the following message:
'Unsorted input from primary source (chr10 < chr9)'

...but my input VCF is sorted as chr1...chr9,chr10...chr22, chrX, chrY.

If I split the original VCF in two parts:
-part1: chr1 to chr9
-part2: chr10 to 22, X, and Y
the two output files are correct.

Thanks,

Paolo

--
Paolo Uva
CRS4 Bioinformatica
Loc. Piscina Manna
09010 Pula (CA), Italy
http://www.bioinformatica.crs4.it

--

Digest for gen...@soe.ucsc.edu - 11 updates in 6 topics

"Steve Heitner" <st...@soe.ucsc.edu>: Feb 10 10:56AM -0800

table clinVarBed
"Browser extensible data (12 fields) plus information about a ClinVar entry"
(
string chrom; "Chromosome (or contig, scaffold, etc.)"
uint chromStart; "Start position in chromosome"
uint chromEnd; "End position in chromosome"
string name; "Name of item"
uint score; "Score from 0-1000"
char[1] strand; "+ or -"
uint thickStart; "Start of where display should be thick (start codon)"
uint thickEnd; "End of where display should be thick (stop codon)"
uint reserved; "Used as itemRgb as of 2004-11-22"
int blockCount; "Number of blocks"
int[blockCount] blockSizes; "Comma separated list of block sizes"
int[blockCount] chromStarts; "Start positions relative to chromStart"
lstring origName; "Orignal name of item"
string type; "Type of Variant"
string geneId; "NCBI Entrez Gene ID"
string geneSym; "NCBI Entrez Gene Symbol"
string clinSign; "Clinical significance"
string snpId; "dbSNP ID"
string nsvId; "dbVar ID"
string rcvAcc; "ClinVar ID"
string testedInGtr; "Genetic Testing Registry"
lstring phenotype; "Phenotype identifiers"
string origin; "Data origin"
string assembly; "Genome assembly"
string cytogenetic; "Cytogenetic status"
string reviewStatus; "Review status"
lstring hgvsCod; "coding HGVS"
lstring hgvsProt; "protein HGVS"
string numSubmit; "number of submitters"
string lastEval; "last evaluation"
string guidelines; "guidelines"
lstring otherIds; "other identifiers e.g. OMIM IDs, etc."
)

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To unsubscribe from this group and stop receiving emails from it send an email to genome+un...@soe.ucsc.edu.

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robert kuhn

unread,

Feb 11, 2015, 1:43:10 PM2/11/15

to Rupert, David, gen...@soe.ucsc.edu, ku...@soe.ucsc.edu, Hasi, Minire, Cody, Jannine D

Hello, David,

Thanks for your question. I see by using the Table Browser to
download your data, that you have the 9th (itemRgb) column of your
BED file properly encoding your colors. However, for the Genome
Browser to display your chosen colors, you need to enable this feature
using "itemRgb=on" in the track header.

You can find this information in our documentation on this page:

http://genome.ucsc.edu/FAQ/FAQformat.html#format1

Best wishes, and thanks for being a Browser user.

--b0b kuhn
ucsc genome bioinformatics group

On 2/11/2015 9:27 AM, Rupert, David wrote:
>
> I have 2 text files for Chromosome 18 p- work and want to color code
> each gene track with 1 of 5 colors and set it to “Pack”. The info
> pages show that with pack you get the option for a range of greys or
> blues or browns only
>
> Text file “hg19-p-_pack” has the upper section colored as we want,
> but, keeping the coloring, can we display it like the below section,
> the more compact format?
>
> http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr18%3A1-17176994&hgsid=411456277_Sc7n6zdsTmmJQvpPO50peNKF7IQc
>
>
> Text file “hg19-p-_pack2_test” uses the pack layout but only shows grey.
>
> http://genome.ucsc.edu/cgi-bin/hgTracks?db=hg19&position=chr18%3A1-17307123&hgsid=411456493_nOuzCdGDFJlXalL68NS4Mi64fDSO
>
>
> David C. Rupert
>
> MED 540F.1
>
> O-210-567-5251
>
> C- 210-452-6536
>

> *"Happiness equals reality minus expectations"**Tom Magliozzi*
>
> *From:*gen...@soe.ucsc.edu [mailto:gen...@soe.ucsc.edu]
> *Sent:* Wednesday, February 11, 2015 11:12 AM
> *To:* Digest recipients
> *Subject:* [genome] Digest for gen...@soe.ucsc.edu - 9 updates in 7 topics
>
> gen...@soe.ucsc.edu
> <%20%20https:/groups.google.com/a/soe.ucsc.edu/forum/?utm_source=digest&utm_medium=email#%21forum/genome/topics>
>
>
>
>
> Google Groups
> <https://groups.google.com/a/soe.ucsc.edu/forum/?utm_source=digest&utm_medium=email/#%21overview>
>
>
>
>
> <https://groups.google.com/a/soe.ucsc.edu/forum/?utm_source=digest&utm_medium=email/#%21overview>

>
> Topic digest
> View all topics

> <%20%20https:/groups.google.com/a/soe.ucsc.edu/forum/?utm_source=digest&utm_medium=email#%21forum/genome/topics>
>
>
> ·dbsnp of MAF less than 1 percentage <#group_thread_0> - 1 Update
>
> ·downloading a table with cell line information <#group_thread_1> - 3
> Updates
>
> ·reciprocal best hit <#group_thread_2> - 1 Update
>
> ·registering a track hub with UCSC <#group_thread_3> - 1 Update
>
> ·genome browser <#group_thread_4> - 1 Update
>
> ·Variant Annotation Integrator - phyloP100 issue <#group_thread_5> - 1

> Update
>
> ·Digest for gen...@soe.ucsc.edu - 11 updates in 6 topics

> <#group_thread_6> - 1 Update

>
> dbsnp of MAF less than 1 percentage

> <http://groups.google.com/a/soe.ucsc.edu/group/genome/t/4681e741f94bca9f?utm_source=digest&utm_medium=email>
>
> Matthew Speir <msp...@soe.ucsc.edu <mailto:msp...@soe.ucsc.edu>>: Feb

> 10 02:42PM -0800
>
> Hi Alva,
>
> I'm assuming that you are downloading your "snp141Common" data from the
> Table Browser, http://genome.ucsc.edu/cgi-bin/hgTables?db=hg19, or from
> our download server, http://hgdownload.soe.ucsc.edu/downloads.html. To
> get SNP data for hg19 from the Table Browser, just ensure that have
> selected hg19 from the "assembly" drop-down menu on the Table Browser.
> If you are downloading SNP data from our downloads server, you should
> see "hg19" in the URL like so
> http://hgdownload.soe.ucsc.edu/goldenPath/*hg19*/database/snp141Common.txt.gz.
>
>
>
> Please also note that some alleles, such as rs376643643, have no
> frequency data reported at all. The alleleNs and alleleFreqs, or 24th
> and 25th columns, will be empty if there are no frequency data
> available. For example, you can see the alleleNs and alleleFreqs columns
> from the rs376643643 entry in snp141 are empty:
>
> +-------------+----------+-------------+
> | name | alleleNs | alleleFreqs |
> +-------------+----------+-------------+
> | rs376643643 | | |
> +-------------+----------+-------------+
>
> I hope this is helpful. If you have any further questions, please reply

> to gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>. All messages sent

> to that address are archived
> on a publicly-accessible Google Groups forum. If your question includes
> sensitive data, you may send it instead to genom...@soe.ucsc.edu

> <mailto:genom...@soe.ucsc.edu>.

>
> Matthew Speir
> UCSC Genome Bioinformatics Group
>
>
> On 2/6/15 3:54 AM, Rani James, Alva wrote:
>

> Back to top <#digest_top>

>
> downloading a table with cell line information

> <http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d0044c51aa9a03f8?utm_source=digest&utm_medium=email>
>
> Eric Foss <ef...@fredhutch.org <mailto:ef...@fredhutch.org>>: Feb 10

> 01:02PM -0800
>
> Dear UCSC Genome Browser,
>
> You have a page with information about many cell lines here:
>
> http://genome.ucsc.edu/ENCODE/cellTypes.html
> <http://genome.ucsc.edu/ENCODE/cellTypes.html>
>
> Can I download this as a table?
>
> Thank you.
>
> Eric
>

> Brian Lee <bria...@soe.ucsc.edu <mailto:bria...@soe.ucsc.edu>>: Feb

> <mailto:gen...@soe.ucsc.edu>. All

> messages sent to that address are archived on a publicly-accessible forum.
> If your question includes sensitive data, you may send it instead to

> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>.

>
> All the best,
>
> Brian Lee
> UCSC Genome Bioinformatics Group
>

> Brian Lee <bria...@soe.ucsc.edu <mailto:bria...@soe.ucsc.edu>>: Feb

> 10 02:08PM -0800
>
> Dear Eric,
>
> In case it might be of interest, I forgot to add that you can add several
> cv.ra terms to the hgEncodeVocab CGI.
>
> Below are two links, one for hg19 and one for mm9, where all the distinct
> cell terms from the related metadata tables have been put into a URL, each
> with a comma (term=X,Y,Z) providing a type of table seen on the cellTypes
> page:
> mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -Ne 'select
> distinct val from metaDb where var like "cell";' hg19
>
> http://genome.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&deprecated=true&term=8988T,A549,Adult_CD4_Th0,Adult_CD4_Th1,AG04449,AG04450,AG09309,AG09319,AG10803,AoAF,AoSMC,Astrocy,BC_Adrenal_Gland_H12803N,BC_Brain_H11058N,BC_Breast_02-03015,BC_Jejunum_H12817N,BC_Kidney_01-11002,BC_Left_Ventricle_N41,BC_Leukocyte_UHN00204,BC_Liver_01-11002,BC_Lung_01-11002,BC_Pancreas_H12817N,BC_
> Pericardium_H12529N,BC_Placenta_UHN00189,BC_Skeletal_Muscle_01-11002,BC_Skeletal_Muscle_H12817N,BC_Skin_01-11002,BC_Small_Intestine_01-11002,BC_Stomach_01-11002,BC_Testis_N30,BC_Uterus_BN0765,BE2_C,BG02ES,BJ,bone_marrow_HS27a,bone_marrow_HS5,bone_marrow_MSC,Caco-2,CD20+,CD20+_RO01778,CD20+_RO01794,CD34+_Mobilized,CD4+_Naive_Wb11970640,CD4+_Naive_Wb78495824,Cerebellum_OC,Cerebrum_frontal_OC,Chorion,CLL,CMK,Colo829,Colon_OC,Dnd41,ECC-1,Endometrium_OC,Fibrobl,Fibrobl_GM03348,FibroP,FibroP_AG08395,FibroP_AG08396,FibroP_AG20443,Frontal_cortex_OC,GC_B_cell,Gliobla,GM04503,GM04504,GM06990,GM08714,GM10248,GM10266,GM10847,GM12801,GM12812,GM12813,GM12864,GM12865,GM12866,GM12867,GM12868,GM12869,GM12870,GM12871,GM12872,GM12873,GM12874,GM12875,GM12878,GM12878-XiMat,GM12891,GM12892,GM13976,GM13977,GM15510,GM18505,GM18507,GM18526,GM18951,GM19099,GM19193,GM19238,GM19239,GM19240,GM20000,H1-hESC,H1-neurons,H7-hESC,H9ES,HA-h,HA-sp,HAc,HAEpiC,HAoAF,HAoEC,HBMEC,HBVP,HBVSMC,HCF,HCFaa,HCH,HCM,HConF,HCPEpiC,
> HCT-116,Heart_OC,HEEpiC,HEK293,HEK293-T-REx,HEK293T,HeLa-S3,Hepatocytes,HepG2,HFDPC,HFF,HFF-Myc,HGF,HIPEpiC,HL-60,HMEC,HMEpC,HMF,hMNC-CB,hMNC-PB,hMSC-AT,hMSC-BM,hMSC-UC,HMVEC-dAd,HMVEC-dBl-Ad,HMVEC-dBl-Neo,HMVEC-dLy-Ad,HMVEC-dLy-Neo,HMVEC-dNeo,HMVEC-LBl,HMVEC-LLy,HNPCEpiC,HOB,HPAEC,HPAEpiC,HPAF,HPC-PL,HPDE6-E6E7,HPdLF,HPF,HPIEpC,HRCEpiC,HRE,HRGEC,HRPEpiC,HSaVEC,HSMM,HSMMtube,HSMMtube_FSHD,HSMM_emb,HSMM_FSHD,HT-1080,HTR8svn,Huh-7,Huh-7.5,HUVEC,HVMF,HWP,IMR90,iPS,iPS_CWRU1,iPS_hFib2_iPS4,iPS_hFib2_iPS5,iPS_NIHi11,iPS_NIHi7,Ishikawa,Jurkat,K562,Kidney_OC,LHCN-M2,LNCaP,Lung_OC,M059J,MCF-7,MCF10A-Er-Src,Medullo,Medullo_D341,Melano,Mel_2183,Monocytes-CD14+,Monocytes-CD14+_RO01746,MRT_A204,MRT_G401,MRT_TTC549,Myometr,Naive_B_cell,NB4,NH-A,NHBE,NHBE_RA,NHDF,NHDF-Ad,NHDF-neo,NHEK,NHEM.f_M2,NHEM_M2,NHLF,None,NT2-D1,Olf_neurosphere,Osteobl,ovcar-3,PANC-1,Pancreas_OC,PanIsletD,PanIslets,PBDE,PBDEFetal,PBMC,PFSK-1,pHTE,PrEC,ProgFib,prostate,Psoas_muscle_OC,Raji,RCC_7860,RPMI-7951,RPTEC,RWPE1,SAEC,
> SH-SY5Y,SK-N-MC,SK-N-SH,SK-N-SH_RA,SKMC,Small_intestine_OC,Spleen_OC,Stellate,T-47D,Th1,Th17,Th1_Wb33676984,Th1_Wb54553204,Th2,Th2_Wb33676984,Th2_Wb54553204,Treg_Wb78495824,Treg_Wb83319432,U2OS,U87,UCH-1,Urothelia,WERI-Rb-1,WI-38

> <http://genome.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&deprecated=true&term=8988T,A549,Adult_CD4_Th0,Adult_CD4_Th1,AG04449,AG04450,AG09309,AG09319,AG10803,AoAF,AoSMC,Astrocy,BC_Adrenal_Gland_H12803N,BC_Brain_H11058N,BC_Breast_02-03015,BC_Jejunum_H12817N,BC_Kidney_01-11002,BC_Left_Ventricle_N41,BC_Leukocyte_UHN00204,BC_Liver_01-11002,BC_Lung_01-11002,BC_Pancreas_H12817N,BC_Pericardium_H12529N,BC_Placenta_UHN00189,BC_Skeletal_Muscle_01-11002,BC_Skeletal_Muscle_H12817N,BC_Skin_01-11002,BC_Small_Intestine_01-11002,BC_Stomach_01-11002,BC_Testis_N30,BC_Uterus_BN0765,BE2_C,BG02ES,BJ,bone_marrow_HS27a,bone_marrow_HS5,bone_marrow_MSC,Caco-2,CD20+,CD20+_RO01778,CD20+_RO01794,CD34+_Mobilized,CD4+_Naive_Wb11970640,CD4+_Naive_Wb78495824,Cerebellum_OC,Cerebrum_frontal_OC,Chorion,CLL,CMK,Colo829,Colon_OC,Dnd41,ECC-1,Endometrium_OC,Fibrobl,Fibrobl_GM03348,FibroP,FibroP_AG08395,FibroP_AG08396,FibroP_AG20443,Frontal_cortex_OC,GC_B_cell,Gliobla,GM04503,GM04504,GM06990,GM08714,GM10248,GM10266,GM10847,GM12801,GM12812,GM12813,GM12864,GM12865,GM12866,GM12867,GM12868,GM12869,GM12870,GM12871,GM12872,GM12873,GM12874,GM12875,GM12878,GM12878-XiMat,GM12891,GM12892,GM13976,GM13977,GM15510,GM18505,GM18507,GM18526,GM18951,GM19099,GM19193,GM19238,GM19239,GM19240,GM20000,H1-hESC,H1-neurons,H7-hESC,H9ES,HA-h,HA-sp,HAc,HAEpiC,HAoAF,HAoEC,HBMEC,HBVP,HBVSMC,HCF,HCFaa,HCH,HCM,HConF,HCPEpiC,HCT-116,Heart_OC,HEEpiC,HEK293,HEK293-T-REx,HEK293T,HeLa-S3,Hepatocytes,HepG2,HFDPC,HFF,HFF-Myc,HGF,HIPEpiC,HL-60,HMEC,HMEpC,HMF,hMNC-CB,hMNC-PB,hMSC-AT,hMSC-BM,hMSC-UC,HMVEC-dAd,HMVEC-dBl-Ad,HMVEC-dBl-Neo,HMVEC-dLy-Ad,HMVEC-dLy-Neo,HMVEC-dNeo,HMVEC-LBl,HMVEC-LLy,HNPCEpiC,HOB,HPAEC,HPAEpiC,HPAF,HPC-PL,HPDE6-E6E7,HPdLF,HPF,HPIEpC,HRCEpiC,HRE,HRGEC,HRPEpiC,HSaVEC,HSMM,HSMMtube,HSMMtube_FSHD,HSMM_emb,HSMM_FSHD,HT-1080,HTR8svn,Huh-7,Huh-7.5,HUVEC,HVMF,HWP,IMR90,iPS,iPS_CWRU1,iPS_hFib2_iPS4,iPS_hFib2_iPS5,iPS_NIHi11,iPS_NIHi7,Ishikawa,Jurkat,K562,Kidney_OC,LHCN-M2,LNCaP,Lung_OC,M059J,MCF-7,MCF10A-Er-Src,Medullo,Medullo_D341,Melano,Mel_2183,Monocytes-CD14+,Monocytes-CD14+_RO01746,MRT_A204,MRT_G401,MRT>

>
> mysql --user=genome --host=genome-mysql.cse.ucsc.edu -A -Ne 'select
> distinct val from metaDb where var like "cell";' mm9
>
> http://genome.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&deprecated=true&term=10T1/2,3134,416B,A20,Adrenal,B-cell_(CD19+),B-cell_(CD43-),BAT,Bladder,BMDM,B
> oneMarrow,C2C12,Cerebellum,Cerebrum,CH12,CNS,Colon,Cortex,Duodenum,EPC_(CD117+_CD71+_TER119+),EPC_(CD117+_CD71+_TER119-),EPC_(CD117+_CD71-_TER119-),EPC_(CD117-_CD71+_TER119+),EpiSC-5,EpiSC-7,Erythrobl,ES-46C,ES-Bruce4,ES-CJ7,ES-D3,ES-E14,ES-EM5Sox17huCD25,ES-TT2,ES-WW6,ES-WW6_F1KO,FatPad,Fibroblast,ForelimbBud,FrontalLobe,FVLstem,FVprogenitor,G1E,G1E-ER4,GenitalFatPad,HeadlessEmbryo,Heart,HindlimbBud,J185a,Kidney,L1210,LgIntestine,Limb,Liver,Lung,MammaryGland,MEF,Megakaryo,MEL,MEP,Mesoderm,mG/ER,NIH-3T3,OlfactBulb,Ovary,Patski,Placenta,Retina,SkMuscle,SmIntestine,Spleen,Stomach,SubcFatPad,T-Naive,Testis,THelper-Activated,Thymus,TReg,TReg-Activated,WholeBrain,ZhBTc4

> <http://genome.ucsc.edu/cgi-bin/hgEncodeVocab?ra=encode/cv.ra&deprecated=true&term=10T1/2,3134,416B,A20,Adrenal,B-cell_%28CD19+%29,B-cell_%28CD43-%29,BAT,Bladder,BMDM,BoneMarrow,C2C12,Cerebellum,Cerebrum,CH12,CNS,Colon,Cortex,Duodenum,EPC_%28CD117+_CD71+_TER119+%29,EPC_%28CD117+_CD71+_TER119-%29,EPC_%28CD117+_CD71-_TER119-%29,EPC_%28CD117-_CD71+_TER119+%29,EpiSC-5,EpiSC-7,Erythrobl,ES-46C,ES-Bruce4,ES-CJ7,ES-D3,ES-E14,ES-EM5Sox17huCD25,ES-TT2,ES-WW6,ES-WW6_F1KO,FatPad,Fibroblast,ForelimbBud,FrontalLobe,FVLstem,FVprogenitor,G1E,G1E-ER4,GenitalFatPad,HeadlessEmbryo,Heart,HindlimbBud,J185a,Kidney,L1210,LgIntestine,Limb,Liver,Lung,MammaryGland,MEF,Megakaryo,MEL,MEP,Mesoderm,mG/ER,NIH-3T3,OlfactBulb,Ovary,Patski,Placenta,Retina,SkMuscle,SmIntestine,Spleen,Stomach,SubcFatPad,T-Naive,Testis,THelper-Activated,Thymus,TReg,TReg-Activated,WholeBrain,ZhBTc4>

>
> Thank you again for your inquiry and using the UCSC Genome Browser. If you
> have any further questions, please reply to gen...@soe.ucsc.edu

> <mailto:gen...@soe.ucsc.edu>. All

> messages sent to that address are archived on a publicly-accessible forum.
> If your question includes sensitive data, you may send it instead to

> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>.

>
> All the best,
> Brian Lee
>

> Back to top <#digest_top>
>
> reciprocal best hit
> <http://groups.google.com/a/soe.ucsc.edu/group/genome/t/1f63be713742d7ea?utm_source=digest&utm_medium=email>
>
> "Steve Heitner" <st...@soe.ucsc.edu <mailto:st...@soe.ucsc.edu>>: Feb

> 10 01:46PM -0800
>
> Hello, Anaïs.
>
> You should indeed get single coverage. Please ensure that you are
> following the exact procedure. The warning message is probably an
> indication of where the problem is occurring.
>
> Please contact us again at gen...@soe.ucsc.edu

> <mailto:gen...@soe.ucsc.edu> if you have any further questions.

> Questions sent to that address will be archived in a
> publicly-accessible forum for the benefit of other users. If your
> question contains sensitive data, you may send it instead to

> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>.

>
> ---
> Steve Heitner
> UCSC Genome Bioinformatics Group
>
>
>
> From: Anaïs Gouin [mailto:anais...@irisa.fr]
> Sent: Monday, February 09, 2015 6:26 AM
> To: gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>
> Subject: Re: [genome] reciprocal best hit
>
>
>
> A last question to finish. I thought that getting the reciprocal best
> chains would give me only one2one regions.
> By one2one I mean that a region in the first genome match only with
> one other region of the second genome.
>
> But actually here is an example of my reciprocal best pipeline :
>
> chain 237344 scaffold_1 873266 + 56 5232 SFRU_RICE_003848 4548 - 1112
> 4548 24274
> chain 5577 scaffold_1 873266 + 233 5622 SFRU_RICE_003530 4082 - 731
> 3943 31497
>
> Then I have two chains from the same region in scaffold_1 that matches
> with two defferent scaffolds of my second genome.
>
> Can you give me some explanations about the reciprocal best chains please?
>
> Thanks a lot in advance,
>
>
>
> Anaïs
>
>
>
> _____
>

> reply to gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>. All

> messages sent to that address are archived on a publicly-accessible
> Google Groups forum. If your question includes sensitive data, you may
> send it instead to genom...@soe.ucsc.edu

> <mailto:genom...@soe.ucsc.edu>.

> Back to top <#digest_top>

>
> registering a track hub with UCSC

> <http://groups.google.com/a/soe.ucsc.edu/group/genome/t/d7ac3c8ba9ee2120?utm_source=digest&utm_medium=email>
>
> Matthew Speir <msp...@soe.ucsc.edu <mailto:msp...@soe.ucsc.edu>>: Feb

> 10 12:19PM -0800
>
> Hi LaDeana,
>
> Thank you for making this data available! I will be the QA engineer
> tasked with reviewing your assembly hub and later adding it to the list
> of publicly available hubs. If you haven't already, you may also find it
> helpful to read our list of track hub guidelines at
> http://genomewiki.ucsc.edu/index.php/Public_Hub_Guidelines. It contains
> a list of common suggestions and requests that we make of hub providers
> before adding their data to the list. At minimum, we request that each
> track have a description page with contact information (usually an email
> address). Feel free to send us additional questions should you have them
> as you work through those guidelines. I will also review your hub and
> send along some suggested improvements.
>
> I hope this is helpful. If you have any further questions, please reply

> to gen...@soe.ucsc.edu <mailto:gen...@soe.ucsc.edu>. All messages sent

> to that address are archived
> on a publicly-accessible Google Groups forum. If your question includes
> sensitive data, you may send it instead to genom...@soe.ucsc.edu

> <mailto:genom...@soe.ucsc.edu>.

>
> Matthew Speir
> UCSC Genome Bioinformatics Group
>
>
> On 2/7/15 8:57 PM, LaDeana Hillier wrote:
>

> Back to top <#digest_top>
>
> genome browser
> <http://groups.google.com/a/soe.ucsc.edu/group/genome/t/2b2423edf6c12fab?utm_source=digest&utm_medium=email>
>
> Daria Merkurjev <dashame...@gmail.com
> <mailto:dashame...@gmail.com>>: Feb 10 11:11AM -0800

>
> Thank you very much for your help!
>
> Daria.
>
> On Tue, Feb 10, 2015 at 7:22 AM, Enrique Medina-Acosta <
>

> Back to top <#digest_top>

>
> Variant Annotation Integrator - phyloP100 issue

> <http://groups.google.com/a/soe.ucsc.edu/group/genome/t/abab05db1a1a6a5e?utm_source=digest&utm_medium=email>
>
> "Steve Heitner" <st...@soe.ucsc.edu <mailto:st...@soe.ucsc.edu>>: Feb

> <mailto:gen...@soe.ucsc.edu> if you have any further questions.

> Questions sent to that address will be archived in a
> publicly-accessible forum for the benefit of other users. If your
> question contains sensitive data, you may send it instead to

> genom...@soe.ucsc.edu <mailto:genom...@soe.ucsc.edu>.

> Back to top <#digest_top>

>
> Digest for gen...@soe.ucsc.edu - 11 updates in 6 topics

> <http://groups.google.com/a/soe.ucsc.edu/group/genome/t/69681a00a1b25fc9?utm_source=digest&utm_medium=email>
>
> "Steve Heitner" <st...@soe.ucsc.edu <mailto:st...@soe.ucsc.edu>>: Feb

> Back to top <#digest_top>

>
> You received this digest because you're subscribed to updates for this
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> To unsubscribe from this group and stop receiving emails from it send
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