Fwd: [genome] RheMac2 gene locations and alignment to other species

[Ben Evans]

Hi Brooke,

Thank you very much for replying to my query below about accessing the genomic data on the UCSC genome browser.  Your responses were very helpful and I've managed to accomplish everything I wanted to accomplish.

I now have another question; recently a complete sequence of the rhesus macaque Y chromosome was published (Hughes et al. 2012, in Nature).  Is there a way to generate a new axt file from this sequence and a human Y chromosome sequence?  I did find a rhesus/human Y chromosome alignment, but the coordinates of those rhesus Y chromosome are now outdated and the data are incomplete.

Thanks,

Ben

Ben Evans
Biology Department
McMaster University
Life Sciences Building room 328

1280 Main Street West
Hamilton, Ontario L8S4K1
Canada
phone (office/lab) : 905-525-9140 x 26973/27261
fax: 905-522-6066
Lab Website: http://www.biology.mcmaster.ca/faculty/evans/EvansLab/

On 2013-01-07, at 8:15 PM, Brooke Rhead wrote:

Hi Ben,

Sorry for the delay in responding to your question.

Part 1:

You can use the Table Browser: http://genome.ucsc.edu/cgi-bin/hgTables, to retrieve coordinates for exons annotated on rheMac2.  First select a gene track/table, then use the "BED - browser extensible data" output format to limit the coordinates to only exons.  Keep in mind that our table coordinates are zero-based, half-open coordinates; see these links for more info:

http://genome.ucsc.edu/FAQ/FAQtracks.html#tracks1
http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms

BED format is described here:
http://genome.ucsc.edu/FAQ/FAQformat.html#format1

The Table Browser BED output includes the name of the gene and an exon number in the fourth field.

To help you select the gene track you wish to use, you can read a description of each track by clicking on the blue track names on the main Genome Browser page (http://genome.ucsc.edu/cgi-bin/hgTracks).  The tracks in the Genes and Gene Prediction Tracks group vary by source of the data, frequency of updates, and level of manual annotation.  The "Other RefSeq" and "TransMap..." tracks show sequence alignments from other species to the rheMac2 genome.

There is not a track in the rheMac2 genome browser that explicitly annotates conserved regions on rhesus as there is on some of our other assemblies such as human and mouse, but you may want to at least look at the Chain/Net tracks in the Comparative Genomics track group to help determine whether a region is conserved.

Part 2:

Check out the Human Chain/Net track on rheMac2.  Here is a link to the track description: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=rheMac2&g=chainNetHg19.

Downloads for the Chain/Net tracks are available by going to our downloads server: http://hgdownload.cse.ucsc.edu/downloads.html and clicking "Rhesus", then scrolling to "Pairwise Alignments".  The rhesus/human downloads are here: http://hgdownload.cse.ucsc.edu/goldenPath/rheMac2/vsHg19/.  In addition to the track description, you may find this page helpful in understanding chains and nets: http://genomewiki.ucsc.edu/index.php/Chains_Nets.

I hope this information is helpful.  If you have further questions, please reply to gen...@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group



On 12/21/12 9:10 AM, Ben Evans wrote:

Hello,

I have two questions:

(1) I am interested in filtering a vcf file to include (or not include)

data near genes and conserved regions.  Can someone please tell me a

simple way to download the RheMac2 coordinates for all exons and

conserved regions?  Basically I need information like this:

GeneExonchromosomestartstop

Gene1exon112020220602

Gene1exon212120221602

Gene2exon112420224602

etc.

(2) I'd like to access the alignment information for rheMac2 and humans

(or another primate).  I'd like the following information:

RheMac2_chromosome

RheMac2_positionRheMac2_sequenceHuman_hg19_chromosomeHuman_hg19_positionHuman_hg19_sequence

11A11A

12T12G

etc.

Can someone please provide me with some simple directions to download or

generate this information?

Thanks,

Ben

Ben Evans

Biology Department

McMaster University

Life Sciences Building room 328

1280 Main Street West

Hamilton, Ontario L8S4K1

Canada

phone (office/lab) : 905-525-9140 x 26973/27261

fax: 905-522-6066

Lab Website: http://www.biology.mcmaster.ca/faculty/evans/EvansLab/

--

[Brooke Rhead]

Hi Ben,

One of our engineers suggests following this genomewiki page on aligning
entire genomes:

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

but reducing the procedures to just use chrY.

I hope this pages is helpful! If you have further questions, please
contact us again at gen...@soe.ucsc.edu.

--
Brooke Rhead
UCSC Genome Bioinformatics Group

> --
>
>
>