Commits · dbb27c82362e281cabe5e7f5fd3ef8b247be1a82 · UMR GDEC / magatt

May 12, 2020
- keep only one hit with gmap (-n1) · dbb27c82
  Helene Rimbert authored 4 years ago
  
  dbb27c82
May 06, 2020
- now use all isoforms of genes when anchoring genes with gmap only (failed... · 06c403b6
  Helene Rimbert authored 4 years ago
  
  now use all isoforms of genes when anchoring genes with gmap only (failed genes with targeted mapping approache)
  06c403b6
May 04, 2020
- BUG: new rule to deal with genes without valid pair of markers · 168392a6
  Helene Rimbert authored 4 years ago
  
  168392a6
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 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
Feb 10, 2020
- new script extractpepandcheck.sh · f72713da
  Helene Rimbert authored 5 years ago
  
  f72713da
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
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
- 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
- snakemake pipeline for the gmap anchoring and stats · b85ceff5
  Helene Rimbert authored 5 years ago
  
  b85ceff5

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