Commits · e44aeb349cbb7822c41236c91e0dabc6a54bb484 · Chaos / chaos.juicer

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Apr 25, 2021
- updating stats sub · e44aeb34
  Neva C. Durand authored Apr 24, 2021
  
  e44aeb34
- Correcting stats · aac4ecc9
  nchernia authored Apr 24, 2021
  
  aac4ecc9
Apr 24, 2021
- Merge branch 'encode' of https://github.com/aidenlab/juicer into encode · 77f9d854
  nchernia authored Apr 24, 2021
  
  77f9d854
- Updating statistics, changing internal position handling for RE delimited files · 08efd032
  nchernia authored Apr 24, 2021
  
  08efd032
- Updating statistics, changing internal position handling for RE delimited files · 7e2f2b68
  nchernia authored Apr 24, 2021
  
  7e2f2b68
Apr 15, 2021
- removing unnecessary files, updating permissions · d96e8a19
  Neva C. Durand authored Apr 14, 2021
  
  d96e8a19
- Merge branch 'encode' of https://github.com/aidenlab/juicer into encode · 22c5badc
  nchernia authored Apr 14, 2021
  
  22c5badc
- adding in sam threads · 0b4474b3
  nchernia authored Apr 14, 2021
  
  0b4474b3
Apr 14, 2021
- dups_sam issue with files containing nothing to be dedupped · 7d482a7d
  Neva C. Durand authored Apr 13, 2021
  
  7d482a7d
- Adding in the c flag and threads for samtools calls, fixing chimeric deletion problem · 6f4f2c1a
  Neva C. Durand authored Apr 13, 2021
  
  6f4f2c1a
- updating PBS scripts · 94381132
  nchernia authored Apr 13, 2021
  
  94381132
Apr 13, 2021
- Experimenting with PBS without all the wrapping scripts for launch · cd63bca0
  nchernia authored Apr 13, 2021
  
  cd63bca0
- removing some cluster specific flags · 15ee75be
  nchernia authored Apr 13, 2021
  
  15ee75be
- getting rid of error causing slashes · 5cdb1e21
  nchernia authored Apr 12, 2021
  
  5cdb1e21
- 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

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Commits · e44aeb349cbb7822c41236c91e0dabc6a54bb484