Question: Error in HTSeq
gravatar for glady
4 months ago by
glady240 wrote:

Hello, I have performed the mapping of miRNA reads to the mirbase precursor file by SHRiMP. But I'm facing a probem in HTSeq while taking the read counts from the output.sam file.

The error which I'm trying to solve is;

Error occured when processing SAM input (line 2305 of file HBI_10.sam): ("'seq' and 'qualstr' do not have the same length.", 'line 2305 of file HBI_10.sam') [Exception type: ValueError, raised in _HTSeq.pyx:808]

Has anyone of you come across this error? What might be the solution?

rna-seq • 230 views
ADD COMMENTlink written 4 months ago by glady240

Not a solution, rather recommendation - better use featurecounts, faster and more flexible.

ADD REPLYlink written 4 months ago by grant.hovhannisyan1.4k

Somehow read on line 2305 is mangled (if the error message is correct) such that it has sequence and quality strings that are of different length. You could backtrack and see where/what step of the processing that happened.

ADD REPLYlink written 4 months ago by genomax62k

How can we correct this? Because the SAM file was a output of SHRiMP algorithm.

ADD REPLYlink written 4 months ago by glady240
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