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BIMSBbioinfo
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pigx_bsseq
bisulfite sequencing pipeline from fastq to methylation reports
https://bioinformatics.mdc-berlin.de/pigx/
GNU General Public License v3.0
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Docker image
#143
xie186
closed
5 years ago
4
no ranges for Scorematrix
#142
Blosberg
closed
4 years ago
2
Store sm logfiles
#141
Blosberg
closed
5 years ago
0
Comments needed in pigx-bsseq.in
#140
Blosberg
closed
4 years ago
2
Need to be able to print shell commands for final_report rule
#139
Blosberg
closed
4 years ago
13
move snakejob.rule.e/o log files into a subfolder of pigx_work
#138
Blosberg
opened
5 years ago
5
Empty methseg run
#137
Blosberg
closed
6 years ago
0
Add start/stop timestamps to output log
#136
Blosberg
closed
4 years ago
3
Rrbs
#135
Blosberg
closed
6 years ago
1
out/pigx_work/CONTENTS.txt is created as read-only
#134
rekado
closed
6 years ago
0
final report should not be rerun if addtional diffmeth comparisons are requested
#133
alexg9010
closed
6 years ago
1
More description is needed in some of the figures
#132
Blosberg
opened
6 years ago
0
allow for partial resource request specifications
#131
Blosberg
opened
6 years ago
0
sed and grep should be configured
#130
rekado
closed
6 years ago
0
additional qsub args
#129
alexg9010
closed
6 years ago
0
Display current workflow diagram in README
#128
Blosberg
closed
6 years ago
0
UCSC hub
#127
Blosberg
opened
6 years ago
2
consolidate tables in diff_meth chromosome table
#126
Blosberg
closed
4 years ago
2
Polish reports
#125
Blosberg
closed
6 years ago
0
Dedupe patch
#124
Blosberg
closed
6 years ago
0
diffmeth.rmd should be passed hyper/hypo files explicitly
#123
Blosberg
closed
6 years ago
2
polish final reports
#122
Blosberg
closed
6 years ago
1
only take existing samples;
#121
alexg9010
closed
6 years ago
0
Choose sensible defaults for segmentation.
#120
alexg9010
opened
6 years ago
2
Reduce RAM footprint in final report generation
#119
Blosberg
opened
6 years ago
6
Replace pipeline image in the README
#118
Blosberg
closed
6 years ago
3
Put the rules in order
#117
Blosberg
closed
6 years ago
1
fix deduplication for pair-end samples
#116
katwre
closed
6 years ago
2
Add tSSregion plot
#115
Blosberg
closed
6 years ago
0
strange histogram of CpG coverage --problem with deduplication?
#114
Blosberg
closed
6 years ago
5
make distcheck error with older version.
#113
Blosberg
closed
5 years ago
5
Add plots
#112
Blosberg
closed
6 years ago
0
Reorganize bam file storage
#111
katwre
opened
6 years ago
1
Add an option to save unaligned reads
#110
katwre
opened
6 years ago
0
Fix make distcheck
#109
katwre
closed
6 years ago
0
save tabix files
#108
Blosberg
closed
4 years ago
1
Add verbose and shell-command options to argument list
#107
Blosberg
closed
6 years ago
4
export_bw fails with low-coverage data
#106
Blosberg
closed
6 years ago
0
Adjust sample sheet parsing
#105
alexg9010
opened
6 years ago
5
print meaningful error when sample sheet has an extra line
#104
Blosberg
closed
6 years ago
3
Add test dataset to test diff. meth. reports
#103
katwre
closed
4 years ago
2
Please append log (or output) files with "program complete"
#102
Blosberg
closed
4 years ago
0
Fix issue #77; Diff. meth. reports in separate html files
#101
katwre
closed
6 years ago
0
Access bedfile
#100
Blosberg
closed
6 years ago
0
Fixes #85
#99
katwre
closed
6 years ago
0
making standard 'tests' directory (consistent with rnaseq pipeline)
#98
Blosberg
closed
6 years ago
0
Diff meth exceeds memory allowance
#97
Blosberg
closed
6 years ago
1
Run Use-case through pipeline for example figures in docs
#96
Blosberg
closed
6 years ago
1
check that segmentation png file exists; else note omission in report.
#95
Blosberg
closed
6 years ago
1
Cluster q direct
#94
Blosberg
closed
6 years ago
3
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