biomedicalinformaticsgroup/Sargasso
Sargasso disambiguates mixed-species high-throughput sequencing data.
PythonNOASSERTION
Issues
- 7
- 1
Sample names can't end in an underscore
#112 opened by lweasel - 2
Facilitating assessment of ambiguous reads.
#110 opened by sknaack - 9
Error with the parameter test script
#108 opened by katieemelianova - 3
Way to resume running after crash?
#109 opened by katieemelianova - 0
schema 0.3.1 gave error with py3
#104 opened by hxin - 2
Sargasso documentation
#107 opened by blanleung - 1
Critical steps 30-34 for avoiding misinterpretation
#106 opened by mavino - 3
- 1
- 1
bowtie2 parameter bug for dnaseq
#102 opened by hxin - 9
chipseq bowtie2 output mismatch tag is for indivudule read in the pair-end reads case.
#96 opened by hxin - 2
test RNA-seq speed in bisulfite-seq branch
#101 opened by hxin - 5
Clean large file in git history
#100 opened by hxin - 2
- 0
bismark will crash when there is no alignment found. This will crash the make file as the result.
#98 opened by hxin - 0
biamark multi-threads error
#97 opened by hxin - 1
filter violation is check twice for the a filter
#83 opened by hxin - 1
- 0
Final check of documentation prior to v2 release
#94 opened by lweasel - 0
- 0
Check docstrings
#85 opened by lweasel - 0
Update README for v2.
#91 opened by lweasel - 2
some options were overwritten by others
#71 opened by hxin - 0
- 0
Fill in usage message for ChIP-seq separator
#82 opened by lweasel - 0
- 0
filter_reads is not passing the log level setting to filter_control, thus the debug info is never printed
#89 opened by hxin - 0
remove unused code in hit_info.py
#69 opened by hxin - 4
- 1
Check code speed vs latest release.
#87 opened by lweasel - 1
Use different configuration for production/dev
#90 opened by hxin - 0
Add ChIP-seq data to pipeline test.
#80 opened by lweasel - 0
- 1
Fix edge case where no reads map for a species
#53 opened by lweasel - 4
- 0
get_data_type_manager.get_separator() seems to return the same separator instance other than a new instance
#88 opened by hxin - 1
- 2
Check and fix operation under Python 3
#77 opened by lweasel - 3
Adding a <dev> branch as pre-release
#70 opened by hxin - 1
The sambamba view in sort_reads script use all cores available, rather than the number of cores specified
#74 opened by hxin - 3
Check before a version update
#68 opened by hxin - 0
- 1
remove cigar intron check
#66 opened by hxin - 3
- 1
Cope with unequal paired-end read lengths
#55 opened by lweasel - 1
Inconsistent use of mismatches in thresholds
#56 opened by lweasel - 1
- 1
- 0