Hi armonazizi,

From my experience, TSS are not explicitly annotated. In fact, they are usually impossible to identify, but I don't know about mm10. Take a look at the annotation file, and decide what feature you want to select. Let's say the features you want have the 3rd column saying 'transcript' (in .gff format). You can extract them into a sorted BED file like so: $ cat mm10.gff | grep -v '^#' | awk '$3=="transcript"' | cut -f1,4,5 | sort -k1,1 -k2,2n -k3,3n > transcripts.bed

From there, I would recommend using BEDtools intersect for your purpose.

I typically used homer annotatePeaks.pl to find my TSS when I was working with Atac-seq data

http://homer.ucsd.edu/homer/ngs/annotation.html

this gives you a good estimate of the distance of the peak to a TSS and the output is an excel table that can be easily made into a bedfile.

Hope this help! ATAC-seq was a tricky point in my bioinformatics career!