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# Summary Milestone Status Owner Created Updated Priority
320 unexpected bowtie2 unpaired alignment behavior v0.9.0 open 3 days ago 3 days ago 5  
319 Bowtie2 -a option MAPQ scores not 0 or 255; also, question about split references v0.9.0 open 2014-08-07 2014-08-07 5  
318 -u/--qupto arg must be at least 1 v0.9.0 open 2014-07-30 2014-07-31 5  
317 invalid reads in unmapped fastq (missing @ symbol) v0.9.0 open 2014-07-22 2014-08-14 5  
316 (ERR): Expected bowtie2 to be in same directory with bowtie2-align v0.9.0 open 2014-06-12 2014-06-18 5  
310 Incorrect fastq format of --un output v0.9.0 open 2014-05-12 2014-07-31 5  
308 Incorrect lengths in sam header. Sequences missing from output sam file. v0.9.0 open 2014-04-26 2014-04-26 5  
307 Mapping position of a read was out of the reference sequence v0.9.0 open 2014-04-14 2014-04-16 5  
306 Crash without any errors when using --un for PhiX filtering v0.9.0 open 2014-04-07 2014-04-07 5  
304 Uniqueness miscomputed by Ns in Bowtie 1.0.0 v0.9.0 open Ben Langmead 2014-03-19 2014-03-19 5  
303 XS field is the same for best and non-best scoring alignments of a same read v0.9.0 open 2014-03-12 3 days ago 5  
299 bug in detection of redundant alignments with soft-clipping v0.9.0 open 2014-01-11 2014-01-11 5  
298 -a option reports different read matches for two identical repeats in reference v0.9.0 open 2013-12-26 2014-07-13 5  
294 Probleme with Bowtie 2 version 2.1.0 v0.9.0 open Ben Langmead 2013-11-28 2014-07-22 5  
286 Error in quality conversion v2.1.0.0 None open 2013-05-13 2013-05-13 5  
285 Not catching an obvious alignment None open 2013-05-09 2013-05-09 5  
276 bowtie2 -k n parameter doesnt report n matches when n exist None open 2013-02-17 2013-02-18 5  
275 bowtie 2 fails to report read as multi-read in paired mode None open 2013-02-09 2013-02-09 5  
268 bowtie2 overlapping pairs None open 2013-01-20 2013-01-20 5  
267 bowtie2 overlapping pairs None open 2013-01-20 2013-01-20 5  
257 Bowtie 2.0.2 corrupt fastq output None pending 2012-11-08 2012-12-16 5  
256 Bowtie2 slower after 2.0.0.beta6 None open 2012-11-05 2013-01-04 5  
251 -trim5 bases are reported as "M"atching in CIGAR None pending 2012-10-02 2012-12-14 5  
243 Bowtie fails at high -m on some data sets None open 2012-09-20 2012-09-20 5  
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