Commits · 1f1c60757541e7fa711f90f2232267ff85429d94 · GUDMAP_RBK / RNA-seq

Mar 06, 2020
- 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
Feb 17, 2020
- Remove premature rseqc references · ff70cf7f
  Gervaise Henry authored 5 years ago
  
  ff70cf7f
Feb 14, 2020
- Updated queues for some processes based on observed resource usage. · c1d6c6f6
  Jonathan Gesell authored 5 years ago
  
  c1d6c6f6
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
Feb 07, 2020
- Added pytest for makeBigWig. · 9363735e
  Jonathan Gesell authored 5 years ago
  
  9363735e
Feb 04, 2020
- Fix fastqc pytest name · 645546fa
  Gervaise Henry authored 5 years ago
  
  645546fa
Feb 03, 2020
- Add resources to AWS configs · 850d99f8
  Gervaise Henry authored 5 years ago
  
  850d99f8
- 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 CI for fastqc · 8f580cc7
  Gervaise Henry authored 5 years ago
  
  8f580cc7
- 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
- Updated output file names for unit test. · d16e6c86
  Jonathan Gesell authored 5 years ago
  
  d16e6c86
- Added unit testing · a28ab789
  Jonathan Gesell authored 5 years ago
  
  a28ab789
- Pass endness to stranded param · 1902055c
  Gervaise Henry authored 5 years ago
  
  1902055c
Jan 29, 2020
- Fix stranded parse and add 8 cores to trimData · 471380f7
  Gervaise Henry authored 5 years ago
  
  471380f7
- 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 28, 2020
- Remove line testing. As count_lines doesn't work for bam and bai files · 2333e8b4
  Venkat Malladi authored 5 years ago
  
  2333e8b4
- Fix the actual tests · e94986e1
  Venkat Malladi authored 5 years ago
  
  e94986e1
- Change single-end tests to reference correct experiment file. · 6b1e233a
  Venkat Malladi authored 5 years ago
  
  6b1e233a
- Update read comparison and decorator · dbdf865f
  Venkat Malladi authored 5 years ago
  
  dbdf865f
Jan 27, 2020
- Update test_alignReads.py · a3564b7c
  Jonathan Gesell authored 5 years ago
  
  a3564b7c
Jan 24, 2020
- Update workflow/tests/test_alignReads.py · 398747a6
  Jonathan Gesell authored 5 years ago
```
Deleted workflow/tests/test_align.py
```
  398747a6
- Updated test scripts. · de4d2b8b
  Jonathan Gesell authored 5 years ago
  
  de4d2b8b
Jan 23, 2020
- Added requested samtools flags for removing unmapped/double-mapped reads. · 415fa462
  Jonathan Gesell authored 5 years ago
  
  415fa462
- Added utils.py · 88a757f3
  Jonathan Gesell authored 5 years ago
  
  88a757f3
- 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
- Corrected scope-specific error in parseMeta.py · ca261a6b
  Jonathan Gesell authored 5 years ago
  
  ca261a6b
- 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
- Reverted to ensure that Trim step is functional. · f6c9944a
  Jonathan Gesell authored 5 years ago
  
  f6c9944a
Jan 21, 2020
- Actually fixed references · ebb7239c
  Jonathan Gesell authored 5 years ago
  
  ebb7239c