ENCODE-DCC/atac-seq-pipeline

Issues

• Build Genome Database stuck on ebwt loop

  #390 opened 4 days ago by astephen333
  3

• Build genome database for your own genome and

  #414 opened a year ago by Rafaelsoler13
  7

• Failure at atac.read_genome_tsv

  #443 opened 2 months ago by shk44
  0

• Pipeline stuck

  #442 opened 3 months ago by JaskaranNeuro
  0

• How to set the seed when subsampling reads

  #441 opened 4 months ago by Al-Murphy
  1

• build_genome_sh did not finish running

  #440 opened 6 months ago by Glinland
  0

• Running without external network connection

  #403 opened 2 years ago by FrancoisMifsud
  5

• Discrepancy between signal p-value and fold change bigwig tracks around the open regions

  #439 opened 6 months ago by AayushGrover
  0

• If the pipeline can be used when data is from other platforms (eg: DNBSEQ-G400).

  #438 opened 7 months ago by lillianj97
  1

• bam files with replicates

  #437 opened 7 months ago by moshe-olshansky
  1

• Differences in qc when validating installation

  #430 opened 8 months ago by bozidar-obradovic
  3

• Don't need to trim adapters

  #433 opened 8 months ago by feather-W
  0

• Add --ntasks-per-node or --exclusive option for your multi-process jobs.

  #434 opened 9 months ago by feather-W
  0

• Failed on fastqs having identical filename but different path

  #431 opened a year ago by yunhailuo
  3

• The pipeline stalled at "chip.read_genome_tsv" for local backend

  #429 opened a year ago by erhei01
  2

• Confirming that separate conditions/treatments should be analyzed by separate pipelines

  #432 opened 10 months ago by OrangeyO2
  2

• Interpreting result files and selecting files for visualization and DAR analysis

  #413 opened a year ago by Rafaelsoler13
  4

• 'mm10_no_alt_analysis_set_ENCODE.fasta.gz.lock' could not be acquired

  #397 opened 2 years ago by hyjforesight
  2

• Memory Saving: too many large files?

  #428 opened a year ago by Rafaelsoler13
  0

• [Question]: Do reads need to be deduped before FRiP calculation

  #424 opened a year ago by tamuanand
  6

• --read-len selection

  #427 opened a year ago by songxh1996
  0

• two replicates and the combined have different signal

  #426 opened a year ago by HYan-lei
  0

• More than 10 replicates

  #422 opened a year ago by LinearParadox
  3

• Invalid MEMLIMIT unit value with LSF jobs on Linux

  #425 opened a year ago by skoplev
  0

• Encode-atac-seq-pipeline environment can't be found?

  #423 opened a year ago by riteshkc
  0

• Duplicated reproducible peaks

  #407 opened 2 years ago by satroz
  4

• 6 days stuck on task=atac.read_genome_tsv:-1, retry=0, status=Running

  #421 opened a year ago by marlmatos
  0

• Help with running the pipeline

  #419 opened a year ago by Chrisdoan9
  1

• Unable to run the pipeline. invalid jar file error

  #420 opened a year ago by Shashankti
  3

• Reuse the same files in case of error.

  #418 opened a year ago by Rafaelsoler13
  0

• Finished parsing without consuming all tokens

  #415 opened a year ago by LI-Qinyao
  1

• How are DNAse-seq data processed with this pipeline?

  #417 opened a year ago by sufyazi
  0

• How are mitochondrial reads aligned?

  #416 opened a year ago by imk1
  1

• test JSON timing out.

  #389 opened 2 years ago by astephen333
  3

• What should I cite

  #412 opened a year ago by Al-Murphy
  0

• AttributeError: module 'grpc' has no attribute '__version__'

  #411 opened a year ago by Rafaelsoler13
  1

• Multi-architecture docker image

  #410 opened a year ago by jwtobias
  0

• pipeline because javax.net.ssl.SSLException failed

  #409 opened a year ago by sjh996
  1

• Pipeline Fails at Peak Calling

  #408 opened 2 years ago by arianraje
  1

• Job atac.align:0:2 exited with return code 3

  #406 opened 2 years ago by icen234
  4

• Pipeline is stuck on atac.read_genome_tsv:-1 on HPC

  #402 opened 2 years ago by danielcasto
  1

• configparser.NoSectionError: No section: 'defaults'

  #401 opened 2 years ago by mingjianPeng
  1

• conda install fails

  #396 opened 2 years ago by mjkinet
  3

• caper init lsf not supported

  #398 opened 2 years ago by cindyli9888
  1

• ERROR when Validating WDL/inputs/imports with Womtool

  #395 opened 2 years ago by wangxiangxiu
  3

• How to deal with repeat peaks in idr.optimal_peak.narrowPeak

  #394 opened 2 years ago by liu-zhiyang
  2

• Error Running Analysis on DNAnexus Platform (web)

  #393 opened 2 years ago by GitPeruser
  0

• Cannot access sample_R1.trim.srt.bam or sample_R1.trim.srt.no_chrM.samstats.qc: No such file or directory

  #391 opened 2 years ago by liboxun
  2

• Task raise_exception has an invalid runtime attribute memory = !! NOT FOUND !!

  #392 opened 2 years ago by nicolerg
  2

• unable to install hg38

  #388 opened 2 years ago by astephen333
  1