Commits · 2b89cc74994cb331ca0683351248c614a6323b0b · GUDMAP_RBK / RNA-seq

Apr 07, 2020
- Add align sampled data · 2b89cc74
  Gervaise Henry authored 5 years ago
  
  2b89cc74
Mar 24, 2020
- Add getRefInfer · 5ee1ac2c
  Gervaise Henry authored 5 years ago
  
  5ee1ac2c
- Add unit test for downsampleData · 8e3cf6c4
  Gervaise Henry authored 5 years ago
  
  8e3cf6c4
- Add dowsampling trimmed fastqs · 3b4d0255
  Gervaise Henry authored 5 years ago
  
  3b4d0255
Mar 20, 2020
- Updated exit message. · 5acdbca8
  Venkat Malladi authored 5 years ago
  
  5acdbca8
- Code review changes/corrections · 28f1a97f
  Jonathan Gesell authored 5 years ago
  
  28f1a97f
Mar 19, 2020
- Reverted to using SLURM with super queue. · 47e9c3e6
  Jonathan Gesell authored 5 years ago
  
  47e9c3e6
- Changed executor to local for inferMetaData to attempt to run quicker. · 810cfffb
  Jonathan Gesell authored 5 years ago
  
  810cfffb
Mar 18, 2020
- Improved logging and removal of redundant variables. · 1e445926
  Jonathan Gesell authored 5 years ago
  
  1e445926
Mar 16, 2020
- Changed tag from 'gene_id' to 'gene_name' · 3c9c7d4d
  Jonathan Gesell authored 5 years ago
  
  3c9c7d4d
Mar 15, 2020
- Fix spelling errors · 3f71105b
  Venkat Malladi authored 5 years ago
  
  3f71105b
- Added paired end and stranded features to featureCounts. · 387290a1
  Jonathan Gesell authored 5 years ago
  
  387290a1
Mar 14, 2020
- Fix reference input for inferMeta · f774a99c
  Gervaise Henry authored 5 years ago
  
  f774a99c
- Fix dedupBam input of inferMeta · 2beb83ad
  Gervaise Henry authored 5 years ago
  
  2beb83ad
- Use dedupBam for inferMeta · ca8ec578
  Gervaise Henry authored 5 years ago
  
  ca8ec578
- Removed unused script · e5fdb858
  Gervaise Henry authored 5 years ago
  
  e5fdb858
- Add back and update name of reference for inferMeta · e187976f
  Gervaise Henry authored 5 years ago
  
  e187976f
Mar 13, 2020
- Fix trim qc output · 23cfdc21
  Gervaise Henry authored 5 years ago
  
  23cfdc21
- Fix dedup qc output · 31054b21
  Gervaise Henry authored 5 years ago
  
  31054b21
- Add process log files · 1f7e1dc9
  Gervaise Henry authored 5 years ago
  
  1f7e1dc9
- Include optional inner distance histogram data output · 765e5226
  Gervaise Henry authored 5 years ago
  
  765e5226
- Output align bam/bai to tuple, use rawBam for inference, fix failed read · 57220b3a
  Gervaise Henry authored 5 years ago
  
  57220b3a
Mar 12, 2020
- Fix sillier error in align unit ci pytest · 420cede9
  Gervaise Henry authored 5 years ago
  
  420cede9
- Fix silly error in align unit ci pytest · ac502364
  Gervaise Henry authored 5 years ago
  
  ac502364
- Fix deduped unit ci sorted bam/bai prefix · 1e50ff6e
  Gervaise Henry authored 5 years ago
  
  1e50ff6e
- Add bai test to dedup unit ci pytest · f50feedd
  Gervaise Henry authored 5 years ago
  
  f50feedd
- Fix bai in align unit ci pytest · c076037b
  Gervaise Henry authored 5 years ago
  
  c076037b
- Add unit test for inferMetadata · a2a809c7
  Gervaise Henry authored 5 years ago
  
  a2a809c7
- Remove R aggregation · ac21c821
  Gervaise Henry authored 5 years ago
  
  ac21c821
- Clean inference, add tin · 12996d71
  Gervaise Henry authored 5 years ago
  
  12996d71
Mar 09, 2020
- Fix exit for tests in calculateTPM.R · 2c5bbdc1
  Gervaise Henry authored 5 years ago
  
  2c5bbdc1
- Generalize count column earlier · 35a91ea1
  Gervaise Henry authored 5 years ago
  
  35a91ea1
Mar 08, 2020
- Add unit test for makeFeatureCounts · 88c55e12
  Gervaise Henry authored 5 years ago
  
  88c55e12
- Fix tpm r filename · 9663d913
  Gervaise Henry authored 5 years ago
  
  9663d913
Mar 06, 2020
- Add back process · 14784208
  Gervaise Henry authored 5 years ago
  
  14784208
- TEST remove count process · 96a89c3a
  Gervaise Henry authored 5 years ago
  
  96a89c3a
- Add TPM calculation to nf · d0d5114b
  Gervaise Henry authored 5 years ago
  
  d0d5114b
- Remove edgeR from calculateTPM script · 1f1c6075
  Gervaise Henry authored 5 years ago
  
  1f1c6075
- Add rscript to calculate tpm · 44e21870
  Gervaise Henry authored 5 years ago
  
  44e21870
- Added feature counts process. · 6675415d
  Jonathan Gesell authored 5 years ago
  
  6675415d