biomedicalinformaticsgroup Sargasso issues

biomedicalinformaticsgroup / Sargasso

Sargasso disambiguates mixed-species high-throughput sequencing data.

http://biomedicalinformaticsgroup.github.io/Sargasso/

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Sample names can't end in an underscore

#112 lweasel opened 7 months ago
1
Too many unmapped short reads - how to map raw reads instead?

#111 deekshamisri closed 6 months ago
7
Facilitating assessment of ambiguous reads.

#110 sknaack opened 1 year ago
2
Way to resume running after crash?

#109 katieemelianova closed 1 year ago
3
Error with the parameter test script

#108 katieemelianova closed 1 year ago
9
Sargasso documentation

#107 blanleung closed 3 years ago
2
Critical steps 30-34 for avoiding misinterpretation

#106 mavino opened 3 years ago
1
species_separator run as Slurm sbatch job on HPC exists prematurely

#105 rbatorsky opened 4 years ago
3
schema 0.3.1 gave error with py3

#104 hxin closed 2 years ago
0
bismark return different number of mismatch for reads in the same pairs

#103 hxin closed 5 years ago
1
bowtie2 parameter bug for dnaseq

#102 hxin closed 5 years ago
1
test RNA-seq speed in bisulfite-seq branch

#101 hxin opened 5 years ago
2
Clean large file in git history

#100 hxin closed 5 years ago
5
issue with space in the read name in fastq.gz file for bowtie2

#99 hxin opened 5 years ago
2
bismark will crash when there is no alignment found. This will crash the make file as the result.

#98 hxin closed 5 years ago
0
biamark multi-threads error

#97 hxin opened 5 years ago
0
chipseq bowtie2 output mismatch tag is for indivudule read in the pair-end reads case.

#96 hxin closed 5 years ago
9
Dev pre merge

#95 hxin closed 5 years ago
0
Final check of documentation prior to v2 release

#94 lweasel closed 5 years ago
0
Check no unexpected files in repository after v2 merge to master

#93 lweasel closed 5 years ago
1
Confirm that v2 code works with both Python 2 and Python 3.

#92 lweasel closed 5 years ago
4
Update README for v2.

#91 lweasel closed 5 years ago
0
Use different configuration for production/dev

#90 hxin closed 5 years ago
1
filter_reads is not passing the log level setting to filter_control, thus the debug info is never printed

#89 hxin closed 5 years ago
0
get_data_type_manager.get_separator() seems to return the same separator instance other than a new instance

#88 hxin opened 5 years ago
0
Check code speed vs latest release.

#87 lweasel closed 5 years ago
1
Remove RnaSeqHitsChecker/DnaSeqHitsChecker if not needed

#86 lweasel closed 5 years ago
0
Check docstrings

#85 lweasel closed 5 years ago
0
Update GitHub Pages documentation for changes in v2.

#84 lweasel closed 5 years ago
0
filter violation is check twice for the a filter

#83 hxin closed 5 years ago
1
Fill in usage message for ChIP-seq separator

#82 lweasel closed 5 years ago
0
Run python scripts with -O to remove debugging code

#81 lweasel closed 5 years ago
1
Add ChIP-seq data to pipeline test.

#80 lweasel opened 5 years ago
0
double check the function 'check_hits' in hit_checker

#79 hxin opened 5 years ago
0
Chipseq

#78 hxin closed 5 years ago
0
Check and fix operation under Python 3

#77 lweasel closed 6 years ago
2
add parallelization to the map_reads/sort_reads/filter_reads

#76 hxin closed 6 years ago
2
add parallelization to the map_reads/sort_reads/filter_reads

#75 hxin closed 6 years ago
0
The sambamba view in sort_reads script use all cores available, rather than the number of cores specified

#74 hxin closed 6 years ago
1
Clarify documentation for running with > 2 species

#73 lweasel closed 5 years ago
0
add parallelization to the map_reads/sort_reads/filter_reads

#72 hxin opened 6 years ago
4
some options were overwritten by others

#71 hxin closed 5 years ago
2
Adding a <dev> branch as pre-release

#70 hxin closed 6 years ago
3
remove unused code in hit_info.py

#69 hxin closed 5 years ago
0
Check before a version update

#68 hxin closed 6 years ago
3
bug when one of the paired-end read does not map at all

#67 hxin closed 6 years ago
0
remove cigar intron check

#66 hxin closed 6 years ago
1
use the primary hit STAR provides to be the BEST hit within one filter.

#65 hxin closed 6 years ago
1
implement the primary alignment from STAR --outSAMprimaryFlag

#64 hxin closed 6 years ago
1
added an optional parameter to specify the tmp folder when doing sambamba sort, which is by default /tmp

#63 hxin closed 6 years ago
1