kundajelab/chipseq_pipeline

Issues

• JSD error: "RuntimeError: module compiled against API version 0xc but this version of numpy is 0xa"

  #50 opened 4 years ago by liliaevgeniou
  1

• ERROR:root:--extsize must >= 1! and chipseq.bds can not get all replicates go through

  #48 opened 5 years ago by yingsun-ucsd
  25

• mm10

  #49 opened 5 years ago by jloupe
  1

• Citing the AQUAS Pipeline

  #47 opened 6 years ago by mkleyman
  1

• Documentation for macs2?

  #46 opened 6 years ago by concatenize
  2

• Some reps get ERROR:root:--extsize must >= 1!

  #45 opened 6 years ago by jloupe
  2

• Can't download hg19 genome data

  #44 opened 6 years ago by tfchipchip
  2

• pipeline deprecated?

  #43 opened 6 years ago by ceesu
  2

• job submission command

  #40 opened 6 years ago by LiangMa2017
  2

• [fread] Unexpected end of file (bwa_sai2sam_pe_core)

  #38 opened 6 years ago by sbstatgen
  6

• Missing `-c` for `macs2 peakcall` ?

  #42 opened 6 years ago by Avsecz
  1

• [Error] two same tag align file in (z)cat and shuf in pipe

  #41 opened 6 years ago by cjhong
  1

• aquas_chipseq pipline SPP error

  #31 opened 6 years ago by fengyun198503
  6

• SPP error in one replicate

  #22 opened 6 years ago by dgoekbuget
  2

• phantompeakqualtools missing from install_dependencies

  #29 opened 6 years ago by jloupe
  3

• "-q [SLURM_ACCOUNT_NAME]" interpreted as file

  #35 opened 6 years ago by jchap14
  1

• aquas_chipseq pipline idr error

  #30 opened 6 years ago by adroubsa
  4

• Undefined symbol: PyUnicodeUCS2_AsASCIIString

  #24 opened 6 years ago by PFRoux
  12

• more than 2 replicates can not be used for chips_pipeline

  #19 opened 6 years ago by yingsun-ucsd
  3

• MACS2 KeyError

  #15 opened 6 years ago by da-bar
  2

• shuf: end of file

  #34 opened 6 years ago by sbstatgen
  8

• dead loop

  #39 opened 6 years ago by LiangMa2017
  18

• Fatal error: chipseq.bds, line 1354, pos 2. Task/s failed.

  #37 opened 6 years ago by easwaranramamurthy
  4

• ERROR:root:--extsize must >= 1!

  #36 opened 6 years ago by zzy1002081237
  2

• Read length

  #33 opened 7 years ago by jloupe
  2

• Trimmed data-sets

  #32 opened 7 years ago by pixelRaquel
  1

• permission denied / file not found

  #23 opened 7 years ago by michdass
  11

• JSON key error in example config

  #28 opened 7 years ago by kdemuren
  1

• Installing Genomes: TwoBitToFa not found

  #13 opened 7 years ago by AHCChan
  5

• Building custom genome data

  #11 opened 7 years ago by wuwill
  8

• Fatal error: /data/fmao/soft/chipseq_pipeline/modules/graphviz.bds, line 126, pos 18. Trying to access element number 1 from list 'etc' (list size: 1).

  #9 opened 7 years ago by maofengbiao
  1

• .fq extension not removed from prefix in bwa alignement step

  #25 opened 7 years ago by tleonardi
  0

• chipseq pipeline set up

  #27 opened 7 years ago by LiangMa2017
  0

• Suggestion on how to analysis the ChIP-seq data

  #21 opened 7 years ago by yingsun-ucsd
  0

• Fatal error: /TF_chipseq_pipeline/chipseq.bds, line 1529, pos 2. Task/s failed.

  #20 opened 7 years ago by yingsun-ucsd
  5

• NA

  #18 opened 7 years ago by biomystery
  1

• Issue with bds

  #17 opened 7 years ago by urjaswita
  4

• How to modify bds if my SGE cluster using vf=memory,p=n_cpu?

  #16 opened 7 years ago by huboqiang
  1

• Fatal error: TF_chipseq_pipeline/modules/align_bwa.bds, line 87, pos 3. Task/s failed.

  #14 opened 7 years ago by rdali
  22

• phantompeakqual Error in names(cc) < names(otl) :attempt to set an attribute on NULL

  #12 opened 8 years ago by crazyhottommy
  0

• software installation

  #8 opened 8 years ago by wcstcyx
  0

• Crashing on bam_to_bed_atac step

  #2 opened 9 years ago by chrisprobert
  1

• software installation

  #1 opened 9 years ago by daler
  7