Commits · 0f7a1097e68a745f942e2c4e0c55b77f9e99c4bc · Chaos / chaos.juicer

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Jun 30, 2021
- Merge pull request #228 from aidenlab/singleseq · 0f7a1097
  nchernia authored Jun 29, 2021
  0f7a1097
- more afterdedup flag · 97b3ce0d
  Neva C. Durand authored Jun 29, 2021
  
  97b3ce0d
- adding in single end changes · 0df7ef86
  Neva C. Durand authored Jun 29, 2021
  
  0df7ef86
- adding in single alignment classification to check script · d2d18d3e
  Neva C. Durand authored Jun 29, 2021
  
  d2d18d3e
Jun 28, 2021
- adding in read groups, stage of afterdedup; update to usage · 5d9f2df4
  Neva C. Durand authored Jun 28, 2021
  
  5d9f2df4
- using a sort position of interior position for single end, renaming to singleend · c350855c
  Neva C. Durand authored Jun 28, 2021
  
  c350855c
Jun 15, 2021
- calling chimeric_sam from juicer with flag · bd93d167
  nchernia authored Jun 15, 2021
  
  bd93d167
- single seq for chimeric sam changes · d29cdebe
  nchernia authored Jun 15, 2021
  
  d29cdebe
Jun 14, 2021
- merging count 2 · 5fca1828
  Neva C. Durand authored Jun 14, 2021
  
  5fca1828
Jun 11, 2021
- bug fixes, doing sam instead of bam · 59f95a4c
  Neva C. Durand authored Jun 11, 2021
  
  59f95a4c
Jun 10, 2021
- updates for singleend · af9067cf
  nchernia authored Jun 09, 2021
  
  af9067cf
Jun 09, 2021
- make sure chrlen is done correctly · a963d4ac
  nchernia authored Jun 08, 2021
  
  a963d4ac
Jun 08, 2021
- starting process of singleend, just need to revise chimeric now · 38c2ab4c
  nchernia authored Jun 08, 2021
  
  38c2ab4c
Jun 07, 2021
- Merge branch 'encode' of https://github.com/aidenlab/juicer into encode · 90823b64
  Neva C. Durand authored Jun 07, 2021
  
  90823b64
- proper name for file for qc_apa · d1d6da66
  Neva C. Durand authored Jun 07, 2021
  
  d1d6da66
May 27, 2021
- Merge branch 'encode' of https://github.com/aidenlab/juicer into encode · 93cf42e8
  nchernia authored May 26, 2021
  
  93cf42e8
- fix typo · a50c79f1
  nchernia authored May 26, 2021
  
  a50c79f1
May 19, 2021
- updating paths · 6cb20e29
  Neva C. Durand authored May 18, 2021
  
  6cb20e29
- adding in qc_apa flag · 19edb318
  Neva C. Durand authored May 18, 2021
  
  19edb318
- adding multithreads for dedupping · d6e92b5b
  Neva C. Durand authored May 18, 2021
  
  d6e92b5b
- changing incorrect path · bc45819b
  Neva C. Durand authored May 18, 2021
  
  bc45819b
May 15, 2021
- unnecessary line removed · 541a62a7
  Neva C. Durand authored May 14, 2021
  
  541a62a7
- 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

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Commits · 0f7a1097e68a745f942e2c4e0c55b77f9e99c4bc