Commits · 81226095a2e4c7b4de7b51fbc0702abb9517f848 · Chaos / chaos.juicer · GitLab

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Sep 18, 2021
- adding some qc flags, adjusting dups sum for single end · 81226095
  nchernia authored Sep 17, 2021
  
  81226095
Sep 17, 2021
- updated CPU scripts to be consistent with SLURM · 1593fbe5
  Neva C. Durand authored Sep 16, 2021
  
  1593fbe5
- Merge branch 'single_dedup' of https://github.com/aidenlab/juicer into single_dedup · 1fe33682
  Neva C. Durand authored Sep 16, 2021
  
  1fe33682
- Major change to terminology · fb774abb
  Neva C. Durand authored Sep 16, 2021
  
  fb774abb
- adding RG tag for single end, moving the bam job later in thee e sequence · 605341bd
  Neva C. Durand authored Sep 16, 2021
  
  605341bd
- fragstr tag different for single end rt:A:7 so that they are separated within... · a65e8980
  Neva C. Durand authored Sep 16, 2021
  a65e8980
Aug 26, 2021
- assembly handling stats properly; counting mapq properly for single end · eefe2969
  nchernia authored Aug 26, 2021
  
  eefe2969
- Dedupping single end · 339420a3
  Neva C. Durand authored Aug 26, 2021
  
  339420a3
- assembly should not need chrom sizes. no hg19 default. for single end,... · adac7b18
  Neva C. Durand authored Aug 26, 2021
  adac7b18
- Dedupping single end · 06a814a8
  Neva C. Durand authored Aug 26, 2021
  
  06a814a8
Aug 13, 2021
- fixing assumption of two reads for duplicate marking · b8d3581f
  nchernia authored Aug 13, 2021
  
  b8d3581f
- Unique and duplicates now out of both alignable + single ended · d824d725
  Neva C. Durand authored Aug 13, 2021
  
  d824d725
- single dedup · 74ae9e04
  nchernia authored Aug 13, 2021
  
  74ae9e04
Aug 11, 2021
- Fixing cleanup call for --qc flag and RG name · b19b7a77
  Neva C. Durand authored Aug 11, 2021
  
  b19b7a77
Aug 04, 2021
- tweaking sort parameters for SLURM. Adding mode in-situ · 2d435503
  Neva C. Durand authored Aug 04, 2021
  
  2d435503
Jul 30, 2021
- adding memory to sort, adding conversion script · a60561d3
  Neva C. Durand authored Jul 30, 2021
  
  a60561d3
Jul 22, 2021
- Touchfile in chimeric needs to be set. Flags added to samtools sort -... · 2e3e773f
  Neva C. Durand authored Jul 22, 2021
  2e3e773f
Jul 20, 2021
- more updates around qc · 226ac586
  Neva C. Durand authored Jul 19, 2021
  
  226ac586
Jul 19, 2021
- do not run hiccups or arrowhead if in qc mode · a15e9e96
  Neva C. Durand authored Jul 19, 2021
  
  a15e9e96
Jul 10, 2021
- adding methylation mode, small typo fix · 7ff940ce
  Neva C. Durand authored Jul 10, 2021
  
  7ff940ce
Jul 08, 2021
- added qc flag · 1646cb49
  Neva C. Durand authored Jul 08, 2021
  
  1646cb49
- Merge branch 'encode' of https://github.com/aidenlab/juicer into encode · 8c41cdc0
  Neva C. Durand authored Jul 08, 2021
  
  8c41cdc0
- adjustments to paths; do correct things for mnd for single seq · 6bbcdd26
  Neva C. Durand authored Jul 08, 2021
  
  6bbcdd26
Jul 03, 2021
- Update sam_to_mnd.sh · fce5b1f3
  nchernia authored Jul 02, 2021
  fce5b1f3
- Update juicer.sh · 675f153f
  nchernia authored Jul 02, 2021
  675f153f
Jul 02, 2021
- Update juicer.sh · 3adfd823
  nchernia authored Jul 02, 2021
  3adfd823
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

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