Coverage per gene by Exons intervals hg19

mariagrmariagr ZMBHMember
edited April 2015 in Ask the GATK team

Hello ,
I ve been trying to write a script for calculating coverage per gene,unsuccessfully(!) ,and I found now that is nicely done by GATK !
I would very much need to use this calculation of depthOfCoverage for each gene but I cannot find the geneList needed in the format explained here. I have a RefSeq gene list downloaded from UCSC table which contains RefSeq name ,cds_start & end and "chr" information. Is this acceptable? I want to do it for exons falling inside the genes, which I have downloaded from : (phase3),
so this would be my Intervals List. It contains only chr info and start-end.
I have also calculated for my bam files the bedtools-genomecov with option of "bedgraph" ,so I wrote a script to calculate mean coverage for each exon whose reads fall onto. Is the calculation of DepthOfCoverage done in the same principle ?
Moreover I cannot find in UCSC a table which combines RefSeq name with used gene Name. Is it combined in this genesList you provide from GATK?
Can you guide me where I could find the exact url for /humgen/.../geneList.txt or if mine could work ,and if exons table is ok with only these 3 columns ?
I m a registered member, as for writing in the forum. Is there any extra procedure needed to access your database ?
Thanks in advance !

Best Answer


  • mariagrmariagr ZMBHMember
    edited April 2015

    Thanks Geraldine for the immediate answer, I actually have downloaded the Table of UCSC for RefSeq genes.
    But, my basic need is to have a file with Refseq name and geneID on same file, ex : NM_020200 PRTFDC1
    on side-by-side columns so that I can parse by any name, and I didn't find a convenient combination at the UCSC tables, so I thought your genesList would be helpful, if available.
    Anyway, I ll see it through, with refseq tables.
    Thanks :smile:

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