Question: (Closed) genes count in sam file using htseq-count
gravatar for bolbolman2000
5.7 years ago by
United States
bolbolman20000 wrote:

I run the htseq-count

htseq-count -s no <fileName>.sam genes.gtf > counts.txt

And I  got the  following error..

[Malformed SAM line: MRNM == '*' although flag bit &0x0008 cleared", 'line 68 of file sorted_genome_alignments.sam')
  [Exception type: ValueError, raised in _HTSeq.pyx:1323]


please any idea.

rna-seq htseq-count page • 2.7k views
ADD COMMENTlink modified 5.7 years ago by Michael Dondrup47k • written 5.7 years ago by bolbolman20000

Hello bolbolman2000!

Questions similar to yours can already be found at:

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ADD REPLYlink written 5.7 years ago by Michael Dondrup47k
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