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Old 01-29-2014, 07:34 AM   #1
Location: UK

Join Date: Aug 2009
Posts: 38
Default htseq-count error message

I keep getting the following error message when i use the htseq-count

Error occured when processing SAM input (line 9786565):
'pair_alignments' needs a sequence of paired-end alignments
[Exception type: ValueError, raised in]

I sorted my sam files using samtools sort -n

On top of this I also get many warnings saying if i am sure sam file is properly sorted or not?

Do you know what is the error message about?
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