GRO-seq - low Same / Diff strand fold enrichment

Question

[l.uva]

Hi!

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 (http://homer.ucsd.edu/homer/ngs/groseq/groseq.html)

Same/Diff fold enrichment should be high

and

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?

Thanks!