Off topic:genes count in sam file using htseq-count
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9.4 years ago

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?
htseq-count rna-seq • 3.1k views
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