snystrom/cutNrun-pipeline

Issues

• zNormalization

  #46 opened a year ago by mniederhuber
  2

• spike-in normalization of bigwigs fails miserably

  #44 opened 2 years ago by snystrom
  8

• Stop calling MACS2 peaks from ControlDNAPath. Use sample-specific inputs, or MACS default background adjustments.

  #29 opened 5 years ago by snystrom
  33

• Add FrIP score computation

  #43 opened 3 years ago by snystrom
  0

• Alignment stats & genome info stats don't compute at each filtering step

  #42 opened 3 years ago by snystrom
  0

• alignmentStats rules are broken

  #39 opened 3 years ago by snystrom
  0

• envmodules not compatible with run commands

  #40 opened 3 years ago by snystrom
  1

• Environment Modules (new snakemake version feature)

  #22 opened 5 years ago by snystrom
  1

• Fix Readme

  #17 opened 4 years ago by snystrom
  1

• bed files have unusual fragment size distributions

  #13 opened 4 years ago by snystrom
  1

• Allow normalization to arbitrary number of genomes

  #15 opened 4 years ago by snystrom
  1

• Use IDR for pooled peak assessment

  #20 opened 4 years ago by snystrom
  1

• add bbsplit step

  #32 opened 4 years ago by snystrom
  1

• Spike-in using combined genome

  #38 opened 4 years ago by snystrom
  1

• Combine bedgraph -> bigwig steps

  #37 opened 4 years ago by snystrom
  0

• adapter trimming needs modification

  #36 opened 4 years ago by snystrom
  1

• Allow sample-specific negative control

  #31 opened 4 years ago by snystrom
  1

• make fragment size distribution plots

  #18 opened 5 years ago by snystrom
  3

• QC Metrics & Report

  #12 opened 5 years ago by snystrom
  1

• Make dashboard-style summary plot for each sample

  #19 opened 5 years ago by snystrom
  2

• Do not include file paths that don't exist in sampleSheet output

  #35 opened 4 years ago by snystrom
  0

• Ignore test/ directory in multiqc step

  #34 opened 4 years ago by snystrom
  0

• fix .gitignore to not ignore sampleInfo, do ignore raw data

  #33 opened 4 years ago by snystrom
  1

• ignore test/ directory during multiqc step

  #30 opened 5 years ago by snystrom
  0

• check for valid genomes

  #28 opened 5 years ago by snystrom
  0

• reduceFastqScreen threads

  #27 opened 5 years ago by snystrom
  0

• Check that baseNameCols exist in sampleInfo.tsv

  #26 opened 5 years ago by snystrom
  0

• Set `readLen` in sample-specific way

  #25 opened 5 years ago by snystrom
  0

• use config.json to pass parameters instead of snakefile header

  #14 opened 5 years ago by snystrom
  0

• Add columns for final output files to sampleSheet & pooledSampleSheet

  #2 opened 5 years ago by snystrom
  0

• noYUHet

  #4 opened 5 years ago by snystrom
  0

• FragType & NormType aren't correctly detected

  #11 opened 6 years ago by snystrom
  2

• Add FastqScreen step

  #21 opened 5 years ago by snystrom
  1

• merge techincal replicates in sample sheet

  #5 opened 5 years ago by snystrom
  0

• remove --extsize from MACS peak calling

  #9 opened 5 years ago by snystrom
  0

• Aggregate all fastqscreen.txt outputs into single summary table, make final output plot

  #24 opened 5 years ago by snystrom
  0

• Define `threads` in config file

  #23 opened 5 years ago by snystrom
  0

• add rules to make pooled files

  #1 opened 6 years ago by snystrom
  0

• add frag-size dist histogram

  #7 opened 5 years ago by snystrom
  0

• Make sampleSheet & poolSampleSheet outputs within a rule

  #16 opened 5 years ago by snystrom
  0

• set -e in snakemake so stderr and stdout go to different places

  #8 opened 5 years ago by snystrom
  0

• add threshold peak calling

  #10 opened 6 years ago by snystrom
  0

• make bg files temp()

  #6 opened 6 years ago by snystrom
  0

• Don't keep Sam output?

  #3 opened 6 years ago by snystrom
  0