Commits · 47ee15b9be95ffb2b2f32b260b6cbc5bbc52ea55 · IGR-lab / ChIP-seq

Aug 07, 2020
- 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
- compute effective genome size for new assembly · d553fcde
  Laura Cook authored 4 years ago
  
  d553fcde
- rule to compute NRF, PBC1, PBC2 and rule to compute NSC and RSC · 5f3ac1e3
  Laura Cook authored 4 years ago
  
  5f3ac1e3
- first commit · 9f47e352
  Laura Cook authored 4 years ago
  
  9f47e352
Jul 20, 2020
- fix multiqc · 306bbbae
  Laura Cook authored 4 years ago
  
  306bbbae
- 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
- not enough time given to alignment rule so increased this · 25723293
  Laura Cook authored 4 years ago
  
  25723293
- 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
- commit · c35e2d92
  Laura Cook authored 4 years ago
  
  c35e2d92
- 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
- added histone mark · d3eacda9
  Laura Cook authored 4 years ago
  
  d3eacda9
- deleted featureCounts · 7b1d741e
  Laura Cook authored 4 years ago
  
  7b1d741e
- change MAPQ cut off to 30 · d73fbd3e
  Laura Cook authored 4 years ago
  
  d73fbd3e
Jul 09, 2020
- updated · 2e9c096e
  Laura Cook authored 4 years ago
  
  2e9c096e
- updated notes · f56411e7
  Laura Cook authored 4 years ago
  
  f56411e7
- added histone mark to config file to be able to use wildcards for replicate overlapping · d35cd46f
  Laura Cook authored 4 years ago
  
  d35cd46f
- put scripts in a separate folder · 993f54ea
  Laura Cook authored 4 years ago
  
  993f54ea
- first commit. used to overlap peaks from biological replicates · aade4c18
  Laura Cook authored 4 years ago
  
  aade4c18
- added following rules: pool_peaks, overlap_peaks, frip · c3beaa66
  Laura Cook authored 4 years ago
  
  c3beaa66
- removed brackets from print function · 59d1e630
  Laura Cook authored 4 years ago
  
  59d1e630
- added print headings · 217e7446
  Laura Cook authored 4 years ago
  
  217e7446
- added ENCODE guideline to comments · cdbf99f7
  Laura Cook authored 4 years ago
  
  cdbf99f7
- first commit · 3ddbd8c7
  Laura Cook authored 4 years ago
  
  3ddbd8c7
- added pybedtools · c172145d
  Laura Cook authored 4 years ago
  
  c172145d
- added picard complexity metrics · 77fe7dc1
  Laura Cook authored 4 years ago
  77fe7dc1
- updated conda environment instructions · 3ff3f331
  Laura Cook authored 4 years ago
  
  3ff3f331
Jul 03, 2020
- first committ · 87f03a2a
  Laura Cook authored 4 years ago
  
  87f03a2a