Commits · 3c21d7fc3c5f2b6810e9e2b267f9bfc9df4b1480 · IGR-lab / ChIP-seq

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
- 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