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bismark2bedGraph not working when different output directory specified
#18
by FelixKrueger
was closed Feb 10, 2016
feature request: explicit --reference/--genome_folder option
enhancement
#4
by avilella
was closed Nov 25, 2015
report on trying bismark_genome_preparation with bowtie2-2.2.6 and hs38DH
#6
by avilella
was closed Dec 1, 2015
feature request: gzip CpG_report.txt from bismark_methylation_extractor
#7
by avilella
was closed Dec 1, 2015
feature request: cram support for bismark_methylation_extractor
#11
by avilella
was closed Jan 14, 2016
Feature request: Add bismark2summary to the Bismark master
#12
by FelixKrueger
was closed Mar 1, 2016
Bug Report: option
--remove_spaces
appears to cause problems in bismark2bedGraph
#13
by FelixKrueger
was closed Feb 10, 2016
Look into possibility to drop
--no-discordant
for Bowtie 2 mode to support dovetailing of reads
#14
by FelixKrueger
was closed Mar 16, 2016
writes out all the alignments for sequence with multiple alignments
#23
by Shicheng-Guo
was closed Feb 10, 2016
methylation calling in watson and crick helix chain separately
#24
by Shicheng-Guo
was closed Feb 25, 2016
bismark_methylation_extractor only for methylation of CpG
#27
by Shicheng-Guo
was closed Feb 24, 2016
How to understand --ignore --ignore_r2 --ignore_3prime --ignore_3prime_r2
#30
by Shicheng-Guo
was closed Feb 25, 2016
methylation extractor/coverage2cytosine path handling issue
#31
by FelixKrueger
was closed Feb 25, 2016
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