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I have BAM files from an RNA-Seq experiment and for all genes (or a subset) I want to get the number of reads in regions around the TSS (e.g. 2kbp) and the TES (e.g. 2 kbp) and calculate the ratio between them. I was thinking of first creating these regions for each gene and store them in a BED file and then use bedtools intersect with the BAM files to get the reads in these regions. My questions is how would I make such a BED file that contains only the specified regions downstream of the TSS and specified regions upstream of the TSS?

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First of all, you need gene coordinates. You can retrieve them in GTF format from GENCODE or other sources.

Next, extract TSS and TES +/- 2kb windows from each gene, taking in mind that genes can be in the forward or reverse strand. Something like this:

awk -F"\t|\"" -vOFS="\t" '$3=="gene" {
  TSS=($7=="+" ? $4-2000"\t"$4+2000 : $5-2000"\t"$5+2000)
  TES=($7=="+" ? $5-2000"\t"$5+2000 : $4-2000"\t"$4+2000)
  print $1,TSS,$10"_TSS_2kb",0,$7
  print $1,TES,$10"_TES_2kb",0,$7
}' annotation.gtf > tss_tes.bed

Here I used GNU Awk from Bash, but you can write your own solution using Python, R or whatever you like.

Finally, count reads falling in these intervals with your tool of choice (you mentioned bedtools, which is fine).

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