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#275 bowtie 2 fails to report read as multi-read in paired mode

open
nobody
bowtie (175)
5
2013-02-09
2013-02-09
Anonymous
No

Bowtie 2 in paired-end mode, reports both mates as unique, yet the second read is a multi-read for which the XS field is not set. Running bowtie2 in single-end mode works as expected, the field XS is set.

bowtie2 -x dm3 -1 read1.fq -2 read2.fq

read:id 97 chrX 34997 42 50M chrU 1079569 0 AGCTTTATGCTGGAACTGGAGGNCAGCCAGAATGTACGCATTCTTCTTTA B89999*9@F?00?D?;:1111#1C9AF<?<4GAFAC??FD=A;BDD<@@ AS:i:-1 XN:i:0 XM:i:1 XO:i:0 XG:i:0 NM:i:1 MD:Z:22G27 YT:Z:UP
read:id 145 chrU 1079569 0 50M chrX 34997 0 AAGTATTTTATTAAGGGCTGGGCAATTTTGGAGTAGTCTTTTATGTAGCG ?B<99BH?**?*9:1);?9?C?9CA8DIGA3322+++?C:<:B=0==:8: AS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UP

bowtie2 -x dm3 -U read2.fq
read:id 0 chrX 2972581 1 50M * 0 0 CGCTACATAAAAGACTACTCCAAAATTGCCCAGCCCTTAATAAAATACTT :8:==0=B:<:C?+++2233AGID8AC9?C?9?;)1:9*?**?HB99<B? AS:i:0 XS:i:0 XN:i:0 XM:i:0 XO:i:0 XG:i:0 NM:i:0 MD:Z:50 YT:Z:UU

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