Question: GRO-seq - low Same / Diff strand fold enrichment
gravatar for l.moreno.uva
17 months ago by
the Netherlands
l.moreno.uva0 wrote:


By using makeTagDirectory (HOMER) to analyse GRO-seq data, I am getting low value of Same / Diff strand fold enrichment (below 6)

Perhaps, because of this issue, HOMER is returning "Guessing sample is ChIP-Seq" rather than RNA-seq. According to the manual (

Same/Diff fold enrichment should be high


If HOMER doesn't guess the sample is strand specific RNA-Seq, there may be problem with how the data was mapped or with how the file is formatted.

I have this issue for 2 samples out of 10. All the files were processed equally and mapped to the human genome-hg19 using Bowtie2 followed by samtools view/sort.

Any comments why I would expect high values for Same/Diff using GRO-seq data?


ADD COMMENTlink modified 15 months ago by Biostar ♦♦ 20 • written 17 months ago by l.moreno.uva0
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1130 users visited in the last hour