How to obtain sense and antisense read counts from Gro-Seq data

Question

[Sam]

I am looking to obtain read-counts for sense and antisense strands from a GRO-Seq bedgraph file -2000/+2000 from the TSS for a set of genes in 1bp windows. Currently I am using HOMER with the -strand +/- -hist 1 -ghist option, is this appropriate?

Would htseq-count or bedtools coverage be better for this? I'm trying to generate a txt file with the following structure:

• 1st column contain the gene ID
• columns 2 to 4001 contain the number of Sense or Antisense reads respectively per nucleotide surrounding the TSS (+/- 2000bp)