HtSeq count error

Question

[Ron]

Hi all,

I updated to new htseq count and am getting these errors. I was using previous version 0.6.1 and it was working well.

Error occured when reading beginning of SAM/BAM file. 'pysam.csamtools.AlignedRead' object has no attribute 'reference_start' [Exception type: AttributeError, raised in _HTSeq.pyx:1357]

The files have been aligned using STAR-Fusion v0.5.1 (STAR aligner).

Any ideas on this ?Somewhat same error as in this post: Error during htseq-count

Thanks,

Ron

[Kevin Blighe]

The author of the previous thread appeared to suggest that the problem vanished when s/he converted the aligned BAM file into SAM, and then back into BAM. You can do this with samtools view, but I'm not sure why it works exactly.

A possibility is that the contig names expected by HTSeq are different than the ones in your reference file, but I'm not sure

[Ron]

The bam file is working fine with older HTSEQ version 0.6.1, which I was using previously. So I reverted back.

[WouterDeCoster]

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your post but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

[Kevin Blighe]

So, you got it working? A new version of samtools was released relatively recently, by the way, and I believe that it came with a at least major change.

[Ron]

No,I had to revert back to the older version.The newer version still giving me the issue. I think BAM file needs to be modified,in order to get it working with the newer version.