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
17 months ago by
O.rka210 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 • 353 views
ADD COMMENTlink written 17 months ago by O.rka210

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

ADD REPLYlink written 17 months ago by Pierre Lindenbaum130k

Do you know of any tutorials to do this?

ADD REPLYlink written 17 months ago by O.rka210

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

ADD REPLYlink written 17 months ago by Dave Carlson390

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

ADD REPLYlink modified 17 months ago • written 17 months ago by O.rka210
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