How can I use bedtools complement, sam mapping file, and my gtf file to get number of reads for intergenic regions?

Question

[O.rka]

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...

[Pierre Lindenbaum]

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

[O.rka]

Do you know of any tutorials to do this?

[Dave Carlson]

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

https://bedtools.readthedocs.io/en/latest/content/tools/intersect.html

[O.rka]

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