Commits · 5056fca3f669e61be20e90b64c3a09444f1c0fe7 · Chaos / chaos.juicer

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May 15, 2021
- cleanup correctly and do not need ligation junction · 5056fca3
  Neva C. Durand authored May 14, 2021
  
  5056fca3
- removing merged1 · 1075ea97
  Neva C. Durand authored May 14, 2021
  
  1075ea97
- adding cleanup flag · 4ad52f40
  Neva C. Durand authored May 14, 2021
  
  4ad52f40
- changed to removing merged1 · c384f791
  Neva C. Durand authored May 14, 2021
  
  c384f791
May 13, 2021
- adding flags --assembly and --cleanup · 0d00179d
  Neva C. Durand authored May 12, 2021
  
  0d00179d
- typo in call to sam_to_pre · 8a0ae3b1
  Neva C. Durand authored May 12, 2021
  
  8a0ae3b1
- adding assembly flag and cleanup flag · 644ba1a5
  Neva C. Durand authored May 12, 2021
  
  644ba1a5
- typo · 003efad4
  Neva C. Durand authored May 12, 2021
  
  003efad4
- suppress error message on removal · b78e9e0e
  Neva C. Durand authored May 12, 2021
  
  b78e9e0e
- updated chimeric mode to no longer check for fastqs and to just work with sam... · 5cd17d6f
  Neva C. Durand authored May 12, 2021
  5cd17d6f
- Updates to mega.sh to reflect Juicer 2.0 changees · c0e9a8d6
  Neva C. Durand authored May 12, 2021
  
  c0e9a8d6
- do not bother counting if ligation junction is XXXX · 6372275b
  Neva C. Durand authored May 12, 2021
  
  6372275b
- adding K flag to alignment for reproducibility. changing name of merged0 to merged1 for clarity. · 59b3a216
  Neva C. Durand authored May 12, 2021
  
  59b3a216
May 05, 2021
- syntax error · 06801e3c
  Neva C. Durand authored May 04, 2021
  
  06801e3c
- deleting alloc mem that seems to cause issues · c689a399
  nchernia authored May 04, 2021
  
  c689a399
Apr 27, 2021
- removing Perl stats · 5aa2363c
  Neva C. Durand authored Apr 26, 2021
  
  5aa2363c
- More stats update · 6f58ca0d
  Neva C. Durand authored Apr 26, 2021
  
  6f58ca0d
Apr 26, 2021
- update statistics · fe452bdf
  Neva C. Durand authored Apr 26, 2021
  
  fe452bdf
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

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Commits · 5056fca3f669e61be20e90b64c3a09444f1c0fe7