to map hg19 GENCODE gene identifiers to > the corresponding CCDS IDs? This was possible to do in SQL using ccdsKgMap > table but it includes now outdated/obsolete knownGene identifiers

in the hg19 KnownGene track are due to a data processing issue and can be safely ignored. We have reported this issue to EBI. I hope this is helpful. If you have any further questions, please

Hello Jairo, I was able to reproduce the problem. Here is a new screen shot:  The URL is: https://genome.ucsc.edu/cgi-bin/hgTracks?db=

bb (hg38) but i couldn't open it. I > searched on google and tried downloading Blitzmax to read the files but no > success. Do you know which software I can use for the bb file

for human hg38/hg19 and mouse mm10/mm39: NCBI RefSeq: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=refSeqComposite GENCODE: http://genome.ucsc

for human hg38/hg19 and mouse mm10/mm39: - NCBI RefSeq: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=refSeqComposite&position=default - GENCODE: http

work with hg38 data, is to use the more recent alignment which was built directly with ensembl transcripts. The hg19 version of that track was built in 2014, whereas the hg38 was 100-

under Human hg38 BLAT results: "Sorry, no matches found (with a score of at > least 20)." > > Secondly, the link to Primer3Plus under the view menu is greyed out and

Hi, How are you? I am unable to output the files to a readable format. The first attachment is what I have selected, and the output attached is what I

of the knownGene table to limit the number of transcripts to one per gene. You can learn more about this table on the following help page, https://genome.ucsc.edu/FAQ/FAQgenes.html

. For hg38, that can be: *Genes and gene predictions* -> *GENCODE V29* -> *knownGene* And for hg19, that can be: *Genes and gene predictions* -> *GENCODE V39lift37* ->

is "knownGene" AKA "UCSC Genes", which may explain why your BED file output did not cover the entire assembly. Did you want a file with the length of the contigs

for human hg38/hg19 and mouse > mm10/mm39: > > - NCBI RefSeq: http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38& > c=chrX&g=refSeqComposite > - GENCODE

mapping older hg19 gene names onto current hg38 ones. One of our engineers recommends the HUGO Gene Nomenclature Committee (HGNC) resource: https://www.genenames.org/ It does

are no knownGene files for equCab3, such files are found only in databases: hg19, hg38, mm10. You can use the cytoBandIdeo.txt.gz file in place of the cytoBand.txt.gz --Hiram On 11

ensGene, knownGene, etc), you can tell if a transcript is non-coding by looking to see if the thickStart column is equal to the thickEnd column. If thickStart == thickEnd, then this

v32 (knownGene) > > 5. Click "Add" > 6. Click "Choose fields" > 7. Under the "GENCODE v32 (knownGene)" section, select "hg38.

source from knownGene to ncbiRefSeq ( http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&c=chrX&g=refSeqComposite). In this case, you may want to use *ncbiRefSeq

on the knownGene table. This dataset contains splicing variants, so it will contain some redundant entries. This may be more desirable if you want to survey a wider set of regions. You

gbdb/hg38/snp/dbSnp153Common.bb FTO_SNPS Upon reading your question, it sounds like, however, you may be looking for the gene name for a list of SNPS in the 23andMe data format that

us the hg38 coordinates of CD24 (which was on chrY > in HG19) > > > > chr6 106969830 106975465 CD24 > > > > My task is to convert not the whole gene coordinates

updates on hg38 and do not release updated data for hg19. These gene sets have changed and it may be helpful to compare your data with the most up-to-date gene sets. Many people chose to

> > hg38 knownGene Transcript from default gene set in UCSC browser > > Then click the *allow selection from checked tables *at the bottom. You > will now see a new section

about the knownGene annotation pipeline. The knownGene pipeline is no longer maintained and has been functionally replaced by the GENCODE Comprehensive gene sets. You can see this

table for hg38 contains some > isoforms with duplicate gene symbols. This table is a subset of the > GENCODEv29 data, which uses Ensembl IDs as primary keys (eg ENSG*). For >

. The knownGene track for hg38 uses the GENCODE, https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg38&g=knownGene, dataset whereas hg19 uses the UCSC Genes, https://genome

: hgsql hg38 -BN -e 'select chrom, txStart, txEnd from knownGene' > ~/in.bed [hgwdev:~> wc -l in.bed 226811 in.bed [hgwdev:~> time /cluster/home/user/bin/x86_64

from the knownGene table like the one you described you will want to use the "selected fields from primary and related tables" option in the Table Browser: *Table Browser

between our knownGene primary geneIDs and Ensembl geneIDs. UCSC switched our main geneIDs to the Ensembl identifiers about 7 months ago, thus both columns should be the same. If you

that the knownGene table (from the previous example), where these coordinates are pulled from, is in genePred format, and there are some considerations if you are trying to produce