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Old 02-19-2014, 05:08 PM   #2
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Location: Pathum Thani, Thailand

Join Date: Nov 2009
Posts: 190

HTSeq requires that the file is name sorted, but the default sorting of some programs is position sorting. I had the same problem, resorting by name fixed it. I think it can handle paired end and non paired end in the same file (not certain), the problem comes when the name indicates a paired read but the next line is a diferent read.

samtools sort -n in.bam out.sort
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