Skip to content

Issues: FelixKrueger/Bismark

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Clear current search query, filters, and sorts
21 Open 594 Closed
21 Open 594 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Extracting CpA methylation (and potentially other contexts separately)
#139 by ghost was closed Nov 7, 2017
1
Strand orientation
#151 by hmyh1202 was closed Jan 5, 2018
2
CX_report.txt appended twice to output file
#150 by martinjvickers was closed Nov 27, 2017
2
Context change between XM tag and CX report
#149 by martinjvickers was closed Jan 8, 2018
3
gzip: {sample}_pe.bismark.cov.gz: No such file or directory // Bismark_methylation_extraction, paired end reads
#148 by josesovaz was closed Nov 9, 2017
2
bismark2summary suggestion/help
#147 by josesovaz was closed Nov 6, 2017
2
Installation issue
#146 by ClaireXinSun was closed Nov 7, 2017
2
Concordant/discordant/dovetail reads
#145 by josesovaz was closed Nov 8, 2017
4
filter_non_conversion in human genome: what parameters should we choose?
#144 by josesovaz was closed Nov 5, 2017
2
cytosine_report only with data?
#143 by DiegoZavallo was closed Nov 7, 2017
9
Mapping Warning Info
#142 by hmyh1202 was closed Nov 1, 2017
2
Mapping PE reads that overlap
#141 by alexpcheng was closed Nov 6, 2017
14
big genome index mapping failed
#140 by hmyh1202 was closed Apr 20, 2018
7
Time consume
#125 by hmyh1202 was closed Sep 15, 2017
1
Constant increase in threads with comma separated list of input files and --parallel parameter bug
#138 by FelixKrueger was closed Oct 30, 2017
@FelixKrueger
1
Can I mix paired-end and single-end files in the same run?
#137 by DiegoZavallo was closed Oct 24, 2017
3
--merge_CpG fails in the coverage2cytosine
#136 by svrever was closed Oct 21, 2017
15
XM tag when dealing with CIGAR insertions/deletions
#135 by martinjvickers was closed Oct 13, 2017
17
Cannot map PEAR merged reads
#134 by jrmerritt6 was closed Nov 7, 2017
11
bismark_methylation_extractor hangs if samtools path is not specified.
#133 by nick863 was closed Oct 5, 2017
1
copy_bismark_files_for_release does not work from outside Bismark folder.
#132 by nick863 was closed Oct 5, 2017
5
empty BAM file with single-end data
#131 by gunjangala was closed Oct 10, 2017
5
CT SNPs during methylation call
#130 by RoseString was closed Oct 4, 2017
5
coverage2cytosine file handling issues
#129 by rifius was closed Oct 13, 2017
2
coverage2cytosine inconsistent accounting
#127 by vpbrendel was closed Oct 9, 2017
6
ProTip! Find all open issues with in progress development work with linked:pr.