htseq-count no features

[onthefly]

Hi All

I am trying the following pipelie: STAR>>htseq-count>>deseq
However, ht-seq is not giving me any features in 5 (out of 6) of my samples. In one sample, htseq finds features perfectly. The STAR output is similar for each of the samples (approx. 95% uniquely mapped reads). Can anyone suggest what could be the issue?

Best
OTF

[Michael.Ante]

Hi OTF,

this may have a plethora of different reasons. The most common one, is that the gff annotation is not matching the alignment reference.
For instance, in your alignment you see reads mapped to "1" (samtools view) and the gff starts with "chr1".

To help you the most, please post the first lines of your alignment, your gff/gtf file and the command you used to run htse-count.

Cheers,

Michael