Question: Trying to understand knownGene annotation file from UCSC
1
gravatar for jacobsen.jeremy
4.4 years ago by
United States
jacobsen.jeremy40 wrote:

I have Annovar output that gives me a position for a variant from the start of a transcript CDS.  The rna sequences in "knownGeneMrna" include the UTRs.  I am trying to find the start of the CDS  (exclude the first UTR) by using "knownGene.txt" but I don't know what the columns are.  I thought it was the case that column 4 was the start of the transcript and column 6 was the end of the UTR but this does not make sense for certain transcripts (such as uc001abv.1) where the UTR seems to be longer than the transcript itself?

I wonder if somebody could help me with a description of or a link to a description of "knownGene"?

 

Thanks,

Jeremy

snp rna-seq • 1.2k views
ADD COMMENTlink modified 4.4 years ago • written 4.4 years ago by jacobsen.jeremy40
0
gravatar for jacobsen.jeremy
4.4 years ago by
United States
jacobsen.jeremy40 wrote:

Found file schemas here: http://www.ncrna.org/glocal/cgi-bin/hgTables?hgsid=7&hgta_doSchemaDb=hg19&hgta_doSchemaTable=knownGene

ADD COMMENTlink written 4.4 years ago by jacobsen.jeremy40
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