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Showing results of 57

# Summary Milestone Status Owner Created Updated Priority
335 Invalid SAMFLAG for paired alignment v0.9.0 open 2015-05-05 2015-05-05 5  
332 paired-end bowtie with --all --try-hard doesn't report all possibilities v0.9.0 open 2015-04-03 2015-04-03 2  
330 Incorrect mapping positions/TLEN field Bowtie2 (2.2.4) v0.9.0 open 2015-02-25 2015-02-25 5  
317 invalid reads in unmapped fastq (missing @ symbol) v0.9.0 open 2014-07-22 2015-02-24 5  
326 Bowtie 1.1.1 hangs when run on indexes built on databases >15GB v0.9.0 open 2015-01-06 2015-02-17 5  
329 Add library type fr-firststrand to bowtie2 v0.9.0 open 2015-02-11 2015-02-17 1  
328 Incorrect TLEN sign for reverse complement paired reads? v0.9.0 open 2015-02-11 2015-02-17 5  
106 crossbow-1.1.0 Soapsnp.pl line 368 None open 2010-10-22 2015-02-03 5  
304 Uniqueness miscomputed by Ns in Bowtie 1.0.0 v0.9.0 open Ben Langmead 2014-03-19 2015-01-16 5  
298 -a option reports different read matches for two identical repeats in reference v0.9.0 open 2013-12-26 2015-01-08 5  
323 Mapping rate anomaly for fragments slightly greater than maxins v0.9.0 open 2014-11-21 2014-11-24 5  
322 Trimming more than read length causes a crash (bowtie 1.1.1, paired-end) v0.9.0 open 2014-11-09 2014-11-09 5  
320 unexpected bowtie2 unpaired alignment behavior v0.9.0 open 2014-08-19 2014-08-19 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 2014-08-19 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  
294 Probleme with Bowtie 2 version 2.1.0 v0.9.0 open Ben Langmead 2013-11-28 2014-07-22 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  
299 bug in detection of redundant alignments with soft-clipping v0.9.0 open 2014-01-11 2014-01-11 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  
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