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Version 1.2 Causes Improperly Paired Alignments Error in RSEM #52

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DarioS opened this Issue May 29, 2017 · 0 comments

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@DarioS
@DarioS

DarioS commented May 29, 2017

Alignments generated by version 1.2 - but not version 1.0.1 - cause an error to be emitted by rsem-parse-alignments and therefore preventing transcript estimation from going ahead.

rsem-parse-alignments /home2/starfish/RSEM/starfish S1.temp/S1 S1.stat/S1 S1.temp/S1.bam 3 -tag XM
Warning: Detected a read pair whose two mates have different names--3NH4HQ1:246:C59MKACXX:5:1101:2705:2182 and 3NH4HQ1:246:C59MKACXX:5:1101:1263:2096!
Read 3NH4HQ1:246:C59MKACXX:5:1101:2705:2182: The two mates do not align to a same transcript! RSEM does not support discordant alignments.

Another user of RSEM had the exact same problem and he had to abandon Bowtie in favour of kallisto because of this blocker. He also found that the problem could be avoided by using Bowtie 2. Can this regression be fixed in Bowtie 1 by version 1.3?

This was referenced Jul 12, 2017

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