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