Question: How to obtain sense and antisense read counts from Gro-Seq data
gravatar for Sam
4.2 years ago by
United States
Sam90 wrote:

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)
read counts groseq • 1.5k views
ADD COMMENTlink written 4.2 years ago by Sam90
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