Commits · 67f335256fde9474df3b881a1e8af87df6365f6f · Chaos / chaos.juicer

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Apr 13, 2021
- Adding check for final stage · 67f33525
  nchernia authored Apr 12, 2021
  
  67f33525
- Updating PBS to Juicer 2.0, changes to SLURM to be consistent with CPU version · f07fb584
  nchernia authored Apr 12, 2021
  
  f07fb584
Apr 04, 2021
- Adding c flag to samtools merge · c7e140c0
  nchernia authored Apr 03, 2021
  
  c7e140c0
Apr 03, 2021
- Updating SLURM to handle read group · 9f41189f
  Neva C. Durand authored Apr 03, 2021
  
  9f41189f
Apr 02, 2021
- more RG tag stuff · ff481e8c
  Neva C. Durand authored Apr 01, 2021
  
  ff481e8c
Apr 01, 2021
- adjusting for RG flag · e142fbae
  nchernia authored Apr 01, 2021
  
  e142fbae
- Addig RG causes ripple effects · 34c01c46
  nchernia authored Apr 01, 2021
  
  34c01c46
- Adding read group to alignment · de2f31a6
  Neva C. Durand authored Mar 31, 2021
  
  de2f31a6
Mar 31, 2021
- Merge pull request #219 from aidenlab/encode-mss · 70e7cfb7
  nchernia authored Mar 30, 2021
  70e7cfb7
- fix norm default · a79d849e
  Muhammad S Shamim authored Mar 30, 2021
  
  a79d849e
- Merge pull request #218 from aidenlab/encode-mss · 1da6d552
  nchernia authored Mar 30, 2021
  1da6d552
- remove KR · b543bb7a
  Muhammad S Shamim authored Mar 30, 2021
  
  b543bb7a
Mar 30, 2021
- update slurm parameters · ee86244b
  Muhammad S Shamim authored Mar 30, 2021
  
  ee86244b
- update default parameter · 05a0ddfc
  Muhammad S Shamim authored Mar 30, 2021
  
  05a0ddfc
- handle new usage · 41b01f5d
  Muhammad S Shamim authored Mar 29, 2021
  
  41b01f5d
Mar 27, 2021
- Merge pull request #217 from eernst/encode · 43af6757
  nchernia authored Mar 26, 2021
  43af6757
Mar 26, 2021
- Resolves #216 · 80eca072
  eernst authored Mar 26, 2021
  
  80eca072
- Making final stage work in SLURM, permission update to index by chr · 9f609f05
  nchernia authored Mar 25, 2021
  
  9f609f05
Mar 25, 2021
- Some issues corrected around fragment assignment (MT circular chromosome issue) · b4c36542
  nchernia authored Mar 25, 2021
  
  b4c36542
Mar 23, 2021
- Count unique reads correctly · 4e58e70f
  nchernia authored Mar 23, 2021
  
  4e58e70f
- write bam · 5e57f89d
  nchernia authored Mar 23, 2021
  
  5e57f89d
- Major update to Juicer 2.0. Now operates on SAM files · 3c62cd63
  nchernia authored Mar 23, 2021
  
  3c62cd63
- Major update to Juicer 2.0. Now operates on SAM files · 428b55e6
  nchernia authored Mar 23, 2021
  
  428b55e6
Jul 03, 2020
- adding header to mapq0 files · f4cc8e46
  nchernia authored Jul 02, 2020
  
  f4cc8e46
May 12, 2020
- Pulling in master to encode branch · da9b3322
  nchernia authored May 11, 2020
  
  da9b3322
- updating usage. note that none is now the default · d4906482
  nchernia authored May 11, 2020
  
  d4906482
- Change log · 0ecc10e1
  nchernia authored May 11, 2020
  0ecc10e1
May 01, 2020
- Files from @suhas-rao · cab7978b
  Muhammad Saad Shamim authored Apr 30, 2020
  
  cab7978b
Apr 18, 2020
- Update juicer.sh · df12164b
  nchernia authored Apr 17, 2020
  
  View commits for tag 1.5.7 1.5.7
  
  df12164b
Dec 11, 2019
- Last rollback removed a lot of changes in the Juicer 2.0 CPU scripts. Rolling... · 07992b14
  nchernia authored Dec 10, 2019
  07992b14
Nov 25, 2019
- removing repetitive script; the one in misc/ is what should be used · 6403a279
  nchernia authored Nov 25, 2019
  
  6403a279
Nov 13, 2019
- Update custom.md · edbe00da
  Muhammad Saad Shamim authored Nov 13, 2019
  
  edbe00da
- Update bug_report.md · 52847a6a
  Muhammad Saad Shamim authored Nov 13, 2019
  
  52847a6a
Sep 19, 2019
- fixing problem in generate site positions when using Python 3.7 · 8f7177a6
  nchernia authored Sep 19, 2019
  
  8f7177a6
Aug 27, 2019
- Now properly handle quadruple reads. Also eliminated MT check, which was not doing the right thing · c9de8924
  nchernia authored Aug 26, 2019
  
  c9de8924
- added new handling of four way reads to END block · 66e9807c
  nchernia authored Aug 26, 2019
  
  66e9807c
Aug 24, 2019
- Changed chimeric blacklist to handle quadruple reads and eliminate MT exception · a55bfe32
  nchernia authored Aug 23, 2019
  
  a55bfe32
Aug 23, 2019
- merging master into encode branch · 6deb1ee3
  nchernia authored Aug 22, 2019
  
  6deb1ee3
- Major change to chimeric blacklist handling of chimeric reads (3 alignments)... · 2fff94b9
  nchernia authored Aug 22, 2019
  2fff94b9
Aug 09, 2019
- Merge pull request #88 from ecsedi/enhanced-patterns · 7bfdb99a
  nchernia authored Aug 09, 2019
  7bfdb99a

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Commits · 67f335256fde9474df3b881a1e8af87df6365f6f