Question: How can I use bedtools complement, sam mapping file, and my gtf file to get number of reads for intergenic regions?
gravatar for O.rka
7 months ago by
O.rka120 wrote:

I'm trying to use my .sam file from STAR and GTF file with bedtools complement to get the following the number of intergenic reads, the number of genic reads, and the number reads that didn't map at all.

How can I do this? I saw this post which suggested some other tools but I need to do a lot of preprocessing for RNA-SeqQC and would like to use bedtools (and any downstream tool that would be necessary for this process): Does STAR give the reads that were mapped at intergenic regions? How can I get the regions and count reads?

Does anyone know how I would do this?

I converted my sam file to a bed file and ran the following:

bedtools -i mapped.bed -g contig.lengths.tsv

but it doesn't know where the intergenic regions are...

rna-seq • 199 views
ADD COMMENTlink written 7 months ago by O.rka120

bedtools alone doesn't work. there must be a subprogram like 'intersect'

ADD REPLYlink written 7 months ago by Pierre Lindenbaum124k

Do you know of any tutorials to do this?

ADD REPLYlink written 7 months ago by O.rka120

Here is the Bedtools intersect documentation. There are a fairly large number of examples provided.

ADD REPLYlink written 7 months ago by Dave Carlson280

For this would I need to run complement, then intersect?

ADD REPLYlink modified 7 months ago • written 7 months ago by O.rka120
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 675 users visited in the last hour