Commits · d7d436c2fa104d29570bad1668b4105ce71f2ec9 · IGR-lab / ChIP-seq

Sep 11, 2020
- first commit. script to subsample BAM files in a directory · d7d436c2
  Laura Cook authored 4 years ago
  
  d7d436c2
- edit input/output folders to run peak calling pipeline on subsampled BAM files · a8013a64
  Laura Cook authored 4 years ago
  
  a8013a64
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
  
  created separate snakefiles for histone marks as I couldn't get the wildcards to work so had to hardcode one of the rules
  6f7e510a
Aug 28, 2020
- added info on converting to 2bit format · 8661c846
  Laura Cook authored 4 years ago
  
  8661c846
- rule for calculating frip in replicate peaks · 2c2a1db7
  Laura Cook authored 4 years ago
  
  2c2a1db7
- added merged input · 7a33f54e
  Laura Cook authored 4 years ago
  
  7a33f54e
- added input control · f390d4b6
  Laura Cook authored 4 years ago
  
  f390d4b6
- adding merging of input control BAM files · 89deb492
  Laura Cook authored 4 years ago
  
  89deb492
- added frip for comparing replicate peaks to pooled peaks · ae4dda23
  Laura Cook authored 4 years ago
  
  ae4dda23
- 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
- fixed missing quotation marks · 0b647726
  Laura Cook authored 4 years ago
  
  0b647726
- remove merging peak files · 23d6e768
  Laura Cook authored 4 years ago
  
  23d6e768
- call peaks on merged BAM files · 04dbfdab
  Laura Cook authored 4 years ago
  
  04dbfdab
- merge BAM files for replicates · 9d9a5490
  Laura Cook authored 4 years ago
  
  9d9a5490
- added notes from camille · cf889686
  Laura Cook authored 4 years ago
  
  cf889686
- deleted · 01675ce6
  Laura Cook authored 4 years ago
  
  01675ce6
- 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
- use bedtools merge for pooling peaks instead of just concatenating two files · b3e92f87
  Laura Cook authored 4 years ago
  
  b3e92f87
Aug 16, 2020
- update · 746bed15
  Laura Cook authored 4 years ago
  
  746bed15
Aug 07, 2020
- formatting · 2afb49d1
  Laura Cook authored 4 years ago
  
  2afb49d1
- added details in to each step in the snakemake pipeline · 24c71ac3
  Laura Cook authored 4 years ago
  
  24c71ac3
- updated config files · c16c4b68
  Laura Cook authored 4 years ago
  
  c16c4b68
- added exclusion range to cross-correlation · 77cc4eff
  Laura Cook authored 4 years ago
  
  77cc4eff
- added max and min fragment length for spp cross correlation · 47ee15b9
  Laura Cook authored 4 years ago
  
  47ee15b9
Aug 04, 2020
- updated notes · c5960ccf
  Laura Cook authored 4 years ago
  
  c5960ccf
Jul 24, 2020
- updated · da44d6c7
  Laura Cook authored 4 years ago
  
  da44d6c7
- added new cluster config for rule align_trimmed_reads · 392e1659
  Laura Cook authored 4 years ago
  
  392e1659
- minor formatting changes · e897205f
  Laura Cook authored 4 years ago
  
  e897205f
- added section on phantomPeakquals · 4fec3164
  Laura Cook authored 4 years ago
  
  4fec3164
- add section on library complexity ENCODE guidelines · d023d5d9
  Laura Cook authored 4 years ago
  
  d023d5d9