Question: coding sequnce read coun
0
gravatar for ashkan
4.0 years ago by
ashkan110
ashkan110 wrote:

Hi Guys, I asked a question yesterday but did not get my answer and I really need it. I have RNA-seq data and its bam file. I want to get the read count per gene. but the problem is that I need only the read counts in the coding sequence part (I don't need the read counts at 5' and 3' UTRs). if I use Htseq And Feature Count I would get the read count for the transcript. do you guys know how I can get the read count per gene only at the CODING SEQUENCE? thanks

rna-seq • 951 views
ADD COMMENTlink modified 4.0 years ago by WouterDeCoster44k • written 4.0 years ago by ashkan110
0
gravatar for genomax
4.0 years ago by
genomax91k
United States
genomax91k wrote:

You could leave only the entries for stuff you want counts on and take the rest of the lines out of your GTF (is that what you are using) file?

ADD COMMENTlink written 4.0 years ago by genomax91k
0
gravatar for WouterDeCoster
4.0 years ago by
Belgium
WouterDeCoster44k wrote:

You could just remove the UTRs from your gtf file... grep -v

ADD COMMENTlink written 4.0 years ago by WouterDeCoster44k
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