No error message or output

[Hwc941014]

Hello:

I was running ModTect using RNA-seq data and genome from maize. I mapped the paried-end RNA-seq data to the genome (by STAR) and then run ModTect, specifing a chromosome and a region. But it only outputs the headers with no actual values. I tried multiple datasets and got the same result. It did not give error message. Do you know what could be the problem? Thank you so much!

WC

[hanzhang2000]

Hi, I was having the same problem when running ModTect after mapping the paired-end RNA-seq data to the human reference genome (CRCh37, downloaded from NCBI RefSeq) by STAR.

Then when I was checking the GTF file and reference genome (GRCh37) from NCBI RefSeq, I found out that in the column chromosome name, they used NCBI chromosome sequence (e.g. NC_000001.10) instead of 'chr1'. After I specified chromosomes in the region file as NCBI chromosome sequence instead of 'chrN', the ModTect program runs fine. I saw your post so I was wondering if it might be the same issue for you as well. Hope it helps!

[Hwc941014]

Thanks for your comments, Hann-Zhang! I will give it a try.