Commits · e650b43f1affedab10677db29b619219e70847f3 · IGR-lab / ChIP-seq

Sep 23, 2020
- edited snakemake command · e650b43f
  Laura Cook authored 4 years ago
  
  e650b43f
- first commit - subsample BAM files to the desired read number · 1ddac80f
  Laura Cook authored 4 years ago
  
  1ddac80f
Sep 03, 2020
- added -snakefile flag to command to call a specific snakefile · 835656b1
  Laura Cook authored 4 years ago
  
  835656b1
- created separate config files for each histone mark · 7a612622
  Laura Cook authored 4 years ago
  
  7a612622
- created separate snakefiles for histone marks as I couldn't get the wildcards... · 6f7e510a
  Laura Cook authored 4 years ago
  6f7e510a
Aug 28, 2020
- commented out to fix bug later · 03140f12
  Laura Cook authored 4 years ago
  
  03140f12
- change directory · b2d4468b
  Laura Cook authored 4 years ago
  
  b2d4468b
- call peaks rule for pooled replicates · 8e92038c
  Laura Cook authored 4 years ago
  
  8e92038c
- fixed bugs in these rules · c84fbb21
  Laura Cook authored 4 years ago
  
  c84fbb21
- fixed rule all · 994fb238
  Laura Cook authored 4 years ago
  
  994fb238
Aug 27, 2020
- update notes · e4ead735
  Laura Cook authored 4 years ago
  
  e4ead735
- add header · d4f740af
  Laura Cook authored 4 years ago
  
  d4f740af
- pool peaks using bedtools merge instead · 57b3ece0
  Laura Cook authored 4 years ago
  
  57b3ece0
- remove counting number of peaks · 28bc62ed
  Laura Cook authored 4 years ago
  
  28bc62ed
- change pvalue · 862b84b7
  Laura Cook authored 4 years ago
  
  862b84b7
Aug 16, 2020
- update · 746bed15
  Laura Cook authored 4 years ago
  
  746bed15
Jul 20, 2020
- narrowpeak counts · 656f6982
  Laura Cook authored 4 years ago
  
  656f6982
- 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
- 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
- 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
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
- edited directory names · 8f99d7be
  Laura Cook authored 4 years ago
  
  8f99d7be