Commits · 0bae9dff04516b6286543bd772de0b2619af5d8c · IGR-lab / ChIP-seq

Jul 20, 2020
- first commit · 0bae9dff
  Laura Cook authored 4 years ago
  
  0bae9dff
Jul 16, 2020
- updated for histone sample file · d85d9ee5
  Laura Cook authored 4 years ago
  
  d85d9ee5
- removed · 13d94a76
  Laura Cook authored 4 years ago
  
  13d94a76
- not enough time given to alignment rule so increased this · 25723293
  Laura Cook authored 4 years ago
  
  25723293
- first commit - breaking it up to run each histone mark separately · 50704a62
  Laura Cook authored 4 years ago
  
  50704a62
- removed --extend_reads in bamCoverage because mouse data in single-ended... · 8e388bed
  Laura Cook authored 4 years ago
  8e388bed
Jul 15, 2020
- commit · c35e2d92
  Laura Cook authored 4 years ago
  
  c35e2d92
- altered wildcards so that marks and stages can be called independently of sample name · e58434cb
  Laura Cook authored 4 years ago
  
  e58434cb
- add cluster config for overlap peaks rules · 7603eef3
  Laura Cook authored 4 years ago
  
  7603eef3
- edited input sample txt file · 9a517078
  Laura Cook authored 4 years ago
  
  9a517078
- changed to input unfiltered BAM from ENCODE · 3c6041ca
  Laura Cook authored 4 years ago
  
  3c6041ca
- added histone mark · d3eacda9
  Laura Cook authored 4 years ago
  
  d3eacda9
- deleted featureCounts · 7b1d741e
  Laura Cook authored 4 years ago
  
  7b1d741e
- change MAPQ cut off to 30 · d73fbd3e
  Laura Cook authored 4 years ago
  
  d73fbd3e
Jul 09, 2020
- updated · 2e9c096e
  Laura Cook authored 4 years ago
  
  2e9c096e
- updated notes · f56411e7
  Laura Cook authored 4 years ago
  
  f56411e7
- added histone mark to config file to be able to use wildcards for replicate overlapping · d35cd46f
  Laura Cook authored 4 years ago
  
  d35cd46f
- put scripts in a separate folder · 993f54ea
  Laura Cook authored 4 years ago
  
  993f54ea
- first commit. used to overlap peaks from biological replicates · aade4c18
  Laura Cook authored 4 years ago
  
  aade4c18
- added following rules: pool_peaks, overlap_peaks, frip · c3beaa66
  Laura Cook authored 4 years ago
  
  c3beaa66
- removed brackets from print function · 59d1e630
  Laura Cook authored 4 years ago
  
  59d1e630
- added print headings · 217e7446
  Laura Cook authored 4 years ago
  
  217e7446
- added ENCODE guideline to comments · cdbf99f7
  Laura Cook authored 4 years ago
  
  cdbf99f7
- first commit · 3ddbd8c7
  Laura Cook authored 4 years ago
  
  3ddbd8c7
- added pybedtools · c172145d
  Laura Cook authored 4 years ago
  
  c172145d
- added picard complexity metrics · 77fe7dc1
  Laura Cook authored 4 years ago
  77fe7dc1
- updated conda environment instructions · 3ff3f331
  Laura Cook authored 4 years ago
  
  3ff3f331
Jul 03, 2020
- first committ · 87f03a2a
  Laura Cook authored 4 years ago
  
  87f03a2a
- edit dunnart inputs to work for single end mouse reads · d060da95
  Laura Cook authored 4 years ago
  
  d060da95
- added consensus peaks rule · 222588f4
  Laura Cook authored 4 years ago
  
  222588f4
- updated · b19be414
  Laura Cook authored 4 years ago
  
  b19be414
- deleted · 4bfefac5
  Laura Cook authored 4 years ago
  
  4bfefac5
- first commit · cb4a9098
  Laura Cook authored 4 years ago
  
  cb4a9098
- added details to rules · 7696dbff
  Laura Cook authored 4 years ago
  
  7696dbff
- edited directory names · 8f99d7be
  Laura Cook authored 4 years ago
  
  8f99d7be
- update · d99b314b
  Laura Cook authored 4 years ago
  
  d99b314b
- first committ · 0f5409bf
  Laura Cook authored 4 years ago
  
  0f5409bf
Jul 01, 2020
- updated · ecf5c25b
  Laura Cook authored 4 years ago
  
  ecf5c25b
- first commit · 7244b64b
  Laura Cook authored 4 years ago
  
  7244b64b
Jun 23, 2020
- update · 144f827c
  Laura Cook authored 4 years ago
  
  144f827c