HTSeq and paired-end data

[balthasar0810]

Hi,

I am using HTSeq for counting of my paired-end bam files. Some reads in the file do not have mate reads because they have been discarded by trimmomatic for some reasons.

Can HTSeq somehow handle this as I am getting Errors saying "Sequence of paired-end alignments expected, but got single-end alignment."?

Best, Christian

[dpryan]

That's just a warning, you can ignore it. The results will be fine.

[balthasar0810]

It is not. HTSeq throws an error and the program stops.

[dpryan]

Odd, that's normally a warning. You might just switch to featureCounts, which is much faster anyway.

[balthasar0810]

I wrote to the developpers and will post their reply here. Anyway, it is true that featureCounts is incredibly fast and seems to handle the above case very well, thanks!

[Michael.Ante]

Hi Balthasar,

you can also use samtools view -f 3 to get only the mapped reads which are in propper pair and pipe it into htseq-count:

samtools view -f 3 -h mybam.bam | htseq-count -f sam - myannotation.gtf

Cheers,
Mihcael

[sebNGS]

Hi Balthasar,

I wonder if you got any reply from the authors for this problem?

Thanks.
Seb