Commits · ee0ee67d740e865efd97ea78e22e3fa598f7f103 · UMR GDEC / magatt

May 04, 2020
- BUG: remove -w from the fgrep command in the split per chrom rule. This cause... · ee0ee67d
  Helene Rimbert authored 4 years ago
  
  BUG: remove -w from the fgrep command in the split per chrom rule. This cause a bug resulting into empty output
  ee0ee67d
- remove chrom unknown from the pipeline · 90e2a185
  Helene Rimbert authored 4 years ago
  
  90e2a185
Apr 30, 2020
- compare sequence strings for exons/cds/utr features · a8fc2d3d
  Helene Rimbert authored 4 years ago
  
  a8fc2d3d
Mar 20, 2020
- save last modif recalcCoords · a16a78fd
  Helene Rimbert authored 5 years ago
  
  a16a78fd
Mar 05, 2020
- remove leading main() at the end of the script. · dbb390cd
  Helene Rimbert authored 5 years ago
  
  dbb390cd
- refactoring in an OO way. recalc for strand + ok · f494725a
  Helene Rimbert authored 5 years ago
  
  f494725a
Feb 28, 2020
- add recalc of coords from hits on strand + and sequence comparison. · fa8d2c66
  Helene Rimbert authored 5 years ago
  
  fa8d2c66
Feb 26, 2020
- gitignore file fixed · 754b4d63
  Helene Rimbert authored 5 years ago
  
  754b4d63
- add diagrams as PDF · c24d1b37
  Helene Rimbert authored 5 years ago
  
  c24d1b37
Feb 25, 2020
- new script: recalc coords on new refseq · c56a3063
  Helene Rimbert authored 5 years ago
  
  c56a3063
- new feature in micromapping: deal with target length between 2 mapped ISBP markers · 32c97e2e
  Helene Rimbert authored 5 years ago
  
  32c97e2e
- check for invalid ISBP pairs in gmapRescue · 614c7080
  Helene Rimbert authored 5 years ago
  
  614c7080
- main snake rule parallelised per chromosome · ba82479e
  Helene Rimbert authored 5 years ago
  
  ba82479e
Feb 10, 2020
- new script extractpepandcheck.sh · f72713da
  Helene Rimbert authored 5 years ago
  
  f72713da
- new rule splitISBP:task is now parallelised per chromosome · 6132a27f
  Helene Rimbert authored 5 years ago
  
  6132a27f
- bug in mapHomologousRegions shell command: need to use {wildcards.chrom}... · 55131a1a
  Helene Rimbert authored 5 years ago
  
  bug in mapHomologousRegions shell command: need to use {wildcards.chrom} instead of {chrom} in the shell to properly expand the chrom variable
  55131a1a
Feb 07, 2020
- add array of chromosome for parallelisation · 998bc657
  Helene Rimbert authored 5 years ago
  
  998bc657
- parallel upstream and downstream marker per chromosome · ea50b37d
  Helene Rimbert authored 5 years ago
  
  ea50b37d
Jan 17, 2020
- new script gmapRescue.sh · fc95bbb9
  Helene Rimbert authored 5 years ago
  
  fc95bbb9
- Final version of blatMapping pipeline · 13be85a0
  Helene Rimbert authored 5 years ago
  
  13be85a0
Dec 20, 2019
- add blat mapping process and nucmer mappig for failed genes · 73118bff
  Helene Rimbert authored 5 years ago
  
  73118bff
- add snakemake directory to gitignore file · 08df3b90
  Helene Rimbert authored 5 years ago
  
  08df3b90
- add result directory to gitignore file, remove markersIds from mapping pipeline · 7465d454
  Helene Rimbert authored 5 years ago
  
  7465d454
Dec 17, 2019
- new snakemake rule geneAnchoring.smk · 16d31b3b
  Helene Rimbert authored 5 years ago
  
  16d31b3b
Dec 16, 2019
- add indexing of reference sequences with samtools faidx · 479d76b6
  Helene Rimbert authored 5 years ago
  
  479d76b6
- update snakemake rules · 953851b9
  Helene Rimbert authored 5 years ago
  
  953851b9
- revert from nextflow to snakemake · 5b5d9130
  Helene Rimbert authored 5 years ago
  
  5b5d9130
Sep 16, 2019
- new config cluster.json for slurm compatibility · cf4d67c7
  Helene Rimbert authored 5 years ago
  
  cf4d67c7
Sep 04, 2019
- modif recalCoordsFromGmap.py · 8b839a6c
  Helene Rimbert authored 5 years ago
  
  8b839a6c
Jul 10, 2019
- update recalcCoordsFromGmap.py · 8fd794b3
  Helene Rimbert authored 5 years ago
  
  8fd794b3
- reformat gmap.smk · 674db69b
  Helene Rimbert authored 5 years ago
  
  674db69b
- new classification algorithm v2.0 · 14c1b343
  Helene Rimbert authored 5 years ago
  
  14c1b343
Jul 09, 2019
- add option of coverage to check gmap matches · fba93930
  Helene Rimbert authored 5 years ago
  
  fba93930
Jul 05, 2019
- add PDF of graphs and dag · 7c73139a
  Helene Rimbert authored 5 years ago
  
  7c73139a
- update readme · 5b3bf31a
  Helene Rimbert authored 5 years ago
  
  5b3bf31a
- change feature of interest to gene · be559820
  Helene Rimbert authored 5 years ago
  
  be559820
- update readme.md · ce690095
  Helene Rimbert authored 5 years ago
  
  ce690095
- BUG: output directory not detected by snakemake. needed to add directory()... · 32047fe2
  Helene Rimbert authored 5 years ago
  
  BUG: output directory not detected by snakemake. needed to add directory() statement for the gmapstats output.
  32047fe2
- add gmap.smk rules · 9f3e8b06
  Helene Rimbert authored 5 years ago
  
  9f3e8b06
- Update README.md · c6371179
  Helene Rimbert authored 5 years ago
  
  c6371179

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