Commits · 12b9d87f48387c2186281d02f0e09c75a073739f · GUDMAP_RBK / RNA-seq

Mar 26, 2020
- Parallelized inferMetaData's TIN calculation. · 82bac4e7
  Jonathan Gesell authored 5 years ago
  
  82bac4e7
Mar 23, 2020
- Fix infer logic · 28850994
  Gervaise Henry authored 5 years ago
  
  28850994
Mar 20, 2020
- initial commit, untested · af133ded
  Jonathan Gesell authored 5 years ago
  
  af133ded
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
- Remove R aggregation · ac21c821
  Gervaise Henry authored 5 years ago
  
  ac21c821
- Clean inference, add tin · 12996d71
  Gervaise Henry authored 5 years ago
  
  12996d71
Feb 28, 2020
- Mod some infer meta · 4a68865f
  Gervaise Henry authored 5 years ago
  
  4a68865f
Feb 17, 2020
- Remove premature rseqc references · ff70cf7f
  Gervaise Henry authored 5 years ago
  
  ff70cf7f
Feb 14, 2020
- Add infer_experiment.py · 3c12e9c1
  Gervaise Henry authored 5 years ago
  
  3c12e9c1
Feb 12, 2020
- Updated to include reference selection · d9895270
  Jonathan Gesell authored 5 years ago
  
  d9895270
Feb 11, 2020
- Corrected path for hisat2 with new directory names · 00643d40
  Jonathan Gesell authored 5 years ago
  
  00643d40
- Add local ref · df73c7e9
  Gervaise Henry authored 5 years ago
  
  df73c7e9
Feb 10, 2020
- Fix temp comment out reference s3 bucket · bf9d4f71
  Gervaise Henry authored 5 years ago
  
  bf9d4f71
- Add temp local ref location · 770f2860
  Gervaise Henry authored 5 years ago
  
  770f2860
- Add ascii art · 4c87cdef
  Gervaise Henry authored 5 years ago
  
  4c87cdef
Feb 07, 2020
- Added pytest for makeBigWig. · 9363735e
  Jonathan Gesell authored 5 years ago
  
  9363735e
Feb 03, 2020
- Fix outdir for fastqc ci and process · 4ca7cd19
  Gervaise Henry authored 5 years ago
  
  4ca7cd19
- Add fastqc output · 2503d937
  Gervaise Henry authored 5 years ago
  
  2503d937
- Add initial fastqc · f8219ccf
  Gervaise Henry authored 5 years ago
  
  f8219ccf
Jan 30, 2020
- Move endsManual in parseMetadata process from spike to stranded · 6bedccc4
  Gervaise Henry authored 5 years ago
  
  6bedccc4
- Cleanup some ci misses · 529dadea
  Gervaise Henry authored 5 years ago
  
  529dadea
- Pass endness to stranded param · 1902055c
  Gervaise Henry authored 5 years ago
  
  1902055c
Jan 29, 2020
- Fix ci to use downsampled data · 0d58c090
  Gervaise Henry authored 5 years ago
  
  0d58c090
- Fetch references from s3 · 5e8def40
  Gervaise Henry authored 5 years ago
  
  5e8def40
- Initial branch commit, tested and working. · 75c31810
  Jonathan Gesell authored 5 years ago
  
  75c31810
Jan 23, 2020
- Added requested samtools flags for removing unmapped/double-mapped reads. · 415fa462
  Jonathan Gesell authored 5 years ago
  
  415fa462
- Added files necessary for CI of output files. · dda7cf97
  Jonathan Gesell authored 5 years ago
  
  dda7cf97
- Added indexing step to align, verified output files. · 724ecd45
  Jonathan Gesell authored 5 years ago
  
  724ecd45
Jan 22, 2020
- Manually specifying reference directory, need to automate. Also added... · 19918779
  Jonathan Gesell authored 5 years ago
```
Manually specifying reference directory, need to automate.  Also added remaining flags to paired-end align.
```
  19918779
- Updated Hisat2 options, and output of parseMeta. · d92d93f9
  Jonathan Gesell authored 5 years ago
  
  d92d93f9
- Reverted to ensure that Trim step is functional. · 25502c3d
  Jonathan Gesell authored 5 years ago
  
  25502c3d