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6.5 years ago
Ron
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1.2k
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
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
The bam file is working fine with older HTSEQ version 0.6.1, which I was using previously. So I reverted back.
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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.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.
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.