elsasserlab/minute

Issues

• Which bigwig files to produce

  #64 opened a year ago by simonelsasser
  2

• bw file output choice

  #40 opened a year ago by simonelsasser
  4

• Rules unpredictably hanging in SLURM context

  #69 opened a year ago by cnluzon
  3

• Create bin coverage table

  #14 opened 2 years ago by cnluzon
  1

• add deepTools fingerprint

  #37 opened 3 years ago by simonelsasser
  0

• Running snakemake on SLURM hangs if a job's status is not recognized

  #53 opened 4 years ago by cnluzon
  3

• Pipeline crashes for rules with threads parameter higher than available (SLURM)

  #68 opened 4 years ago by cnluzon
  7

• Support mapping against multiple genomes

  #26 opened 4 years ago by marcelm
  8

• controls.tsv

  #43 opened 4 years ago by simonelsasser
  1

• Map reads to rodrep

  #63 opened 4 years ago by cnluzon
  2

• Further suggestions for directory layout

  #58 opened 4 years ago by marcelm
  3

• Remove replicate id from controls.tsv

  #27 opened 4 years ago by marcelm
  1

• Implement scaling groups

  #28 opened 4 years ago by marcelm
  0

• carry scaling group into scalinginfo.txt

  #41 opened 4 years ago by simonelsasser
  0

• filenames a bit long --> "replicate"

  #36 opened 4 years ago by simonelsasser
  2

• Create a scaled.idxstats.txt file

  #9 opened 4 years ago by marcelm
  2

• summary stats

  #39 opened 4 years ago by simonelsasser
  2

• config naming

  #38 opened 4 years ago by simonelsasser
  3

• directory naming

  #49 opened 4 years ago by cnluzon
  1

• grouping intermediate outputs in an intermediate directory

  #54 opened 4 years ago by cnluzon
  1

• Used pooled replicates as the read count normalization reference

  #29 opened 5 years ago by marcelm
  2

• Filter out sequences matching specific patterns at demultiplexing

  #32 opened 5 years ago by cnluzon
  8

• Remove intermediate files option

  #33 opened 5 years ago by cnluzon
  2

• Remove effective_genome_size from configuration

  #25 opened 5 years ago by marcelm
  0

• deepTools --binSize should be always set to 1

  #47 opened 5 years ago by cnluzon
  0

• TDF generation is not really necessary

  #34 opened 5 years ago by cnluzon
  1

• Remove chrom_sizes from configuration

  #24 opened 5 years ago by marcelm
  0

• Run MultiQC in the pipeline

  #30 opened 5 years ago by marcelm
  0

• Group wise graphical output

  #42 opened 5 years ago by simonelsasser
  0

• bamCoverage --extendReads crashes when no default fragment size is provided

  #17 opened 5 years ago by cnluzon
  7

• Output dupmarked stats should come from dedup file

  #18 opened 5 years ago by cnluzon
  0

• Add rule to compute Bowtie2 index if necessary

  #23 opened 5 years ago by marcelm
  1

• Specify location of a reference FASTA in configuration

  #22 opened 5 years ago by marcelm
  1

• Get insert sizes for normalization from insert size metrics

  #10 opened 5 years ago by marcelm
  2

• Estimate specific adaptor content from FASTQ files

  #21 opened 5 years ago by cnluzon
  0

• Deduplication leaves second-mate reads of unmapped first-mate unhandled

  #13 opened 5 years ago by cnluzon
  0

• Extra QC: deepTools PCA and fingerprint plots of alignment files

  #15 opened 5 years ago by cnluzon
  0

• Run bwtool summary

  #12 opened 5 years ago by marcelm
  4

• Picard step crashes if no reads found

  #3 opened 5 years ago by cnluzon
  3

• Demultiplexing rules are anonymous

  #5 opened 5 years ago by cnluzon
  2

• Compute statistics

  #7 opened 5 years ago by marcelm
  1

• Describe controls.tsv in README

  #11 opened 5 years ago by marcelm
  0

• Add scaling/normalization

  #8 opened 5 years ago by marcelm
  2