Commits · 68fe00c7634a7f184a424031401d83f817d2ea53 · IGR-lab / ChIP-seq

Sep 18, 2020
- altered to run on 10M subsampled BAM files · 68fe00c7
  Laura Cook authored 4 years ago
  
  68fe00c7
Sep 11, 2020
- edit input/output folders to run peak calling pipeline on subsampled BAM files · a8013a64
  Laura Cook authored 4 years ago
  
  a8013a64
Aug 28, 2020
- 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
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
- 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
- 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
Jul 24, 2020
- rule to compute NRF, PBC1, PBC2 and rule to compute NSC and RSC · 5f3ac1e3
  Laura Cook authored 4 years ago
  
  5f3ac1e3
Jul 20, 2020
- fix multiqc · 306bbbae
  Laura Cook authored 4 years ago
  
  306bbbae
Jul 15, 2020
- change MAPQ cut off to 30 · d73fbd3e
  Laura Cook authored 4 years ago
  
  d73fbd3e
Jul 09, 2020
- added histone mark to config file to be able to use wildcards for replicate overlapping · d35cd46f
  Laura Cook authored 4 years ago
  
  d35cd46f
- added following rules: pool_peaks, overlap_peaks, frip · c3beaa66
  Laura Cook authored 4 years ago
  
  c3beaa66
- added picard complexity metrics · 77fe7dc1
  Laura Cook authored 4 years ago
  77fe7dc1
Jul 03, 2020
- added consensus peaks rule · 222588f4
  Laura Cook authored 4 years ago
  
  222588f4
- edited directory names · 8f99d7be
  Laura Cook authored 4 years ago
  
  8f99d7be
Jul 01, 2020
- first commit · 7244b64b
  Laura Cook authored 4 years ago
  
  7244b64b