Commits · master · IGR-lab / ChIP-seq

Feb 09, 2022
- workflowr set up · 9fcbf351
  lecook authored 3 years ago
  
  9fcbf351
- set up · 3e115631
  lecook authored 3 years ago
  
  3e115631
- Start workflowr project. · 05f0ea4b
  lecook authored 3 years ago
  
  05f0ea4b
Dec 10, 2021
- annotated · 163ebec9
  lecook authored 3 years ago
  
  163ebec9
- annotations updated · d1ba38f5
  lecook authored 3 years ago
  
  d1ba38f5
Dec 09, 2021
- change filename · 46064998
  lecook authored 3 years ago
  
  46064998
- added annotations · c31dd822
  lecook authored 3 years ago
  
  c31dd822
Dec 07, 2021
- clean up · 744df195
  lecook authored 3 years ago
  
  744df195
- change folders · 37fcbe2a
  lecook authored 3 years ago
  
  37fcbe2a
- rearranging scripts · c99e9c3b
  lecook authored 3 years ago
  
  c99e9c3b
- new SSH key · 667f1943
  lecook authored 3 years ago
  
  667f1943
Sep 14, 2021
- duplicate file · 883e5ba2
  lecook authored 3 years ago
  
  883e5ba2
- updated · 65bae9dc
  lecook authored 3 years ago
  
  65bae9dc
Dec 11, 2020
- first commit · c1ea4c9f
  Laura Cook authored 4 years ago
  
  c1ea4c9f
- added chainCleaner · cb1ef93e
  Laura Cook authored 4 years ago
  
  cb1ef93e
- updated · cd229abf
  Laura Cook authored 4 years ago
  
  cd229abf
Oct 15, 2020
- added links to scripts for lastz ad repeak masker · 3c21d7fc
  Laura Cook authored 4 years ago
  
  3c21d7fc
- first commit · e3dbb9f3
  Laura Cook authored 4 years ago
  
  e3dbb9f3
Sep 24, 2020
- generate commands to run array scripts for lastz and repeatMasker · 175f3640
  Laura Cook authored 4 years ago
  
  175f3640
Sep 23, 2020
- changed directory name to ouput peak calls for 10M reads per sample · 178ada24
  Laura Cook authored 4 years ago
  
  178ada24
- changed directory to call peaks on 10M reads · c25710d6
  Laura Cook authored 4 years ago
  
  c25710d6
- 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
- first commit - script parses a multiFASTA and output a separate fasta file for each sequence header · 708da2b7
  Laura Cook authored 4 years ago
  
  708da2b7
- first commit of conda environment with packages for whole genome alignment · ab960190
  Laura Cook authored 4 years ago
  
  ab960190
- added repeat masking steps · b57ad27d
  Laura Cook authored 4 years ago
  
  b57ad27d
Sep 18, 2020
- altered to run on 10M subsampled BAM files · 68fe00c7
  Laura Cook authored 4 years ago
  
  68fe00c7
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