Commits · b18ab4a33021548912279c70ede19d485fa2ddd3 · UMR GDEC / magatt

May 14, 2020
- convertion of the gff file from GMAP after the rescue of misaligned genes is OK. · d0910f29
  Helene Rimbert authored 4 years ago
  
  d0910f29
- ISBPs are now allowed to have some mismatches in the alignment. parameters... · 00d0109a
  Helene Rimbert authored 4 years ago
  
  ISBPs are now allowed to have some mismatches in the alignment. parameters have been added into the config.yaml file and are used accordingly in the rules and filterBam.py script
  00d0109a
May 12, 2020
- NEW script to recalc coords of rescue with gmap · 2e92a9f9
  Helene Rimbert authored 4 years ago
  
  2e92a9f9
- change permission from 644 to 755 · e64475d7
  Helene Rimbert authored 4 years ago
  
  e64475d7
- New script bin/convertGmapCoords.py to convert gmap results from rescur to... · 12ee8807
  Helene Rimbert authored 4 years ago
  
  New script bin/convertGmapCoords.py to convert gmap results from rescur to pseudochromosome coordinates.
  12ee8807
- 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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