datacarpentry/wrangling-genomics

Issues

• Using -p unnecessarily in all the mkdirs

  #261 opened 6 months ago by sstevens2
  0

• Consider updating the trimming tool to something a bit friendlier

  #232 opened 3 years ago by JCSzamosi
  4

• wrangling-genomics/04-variant_calling: Viewing with IGV - typo

  #215 opened 7 months ago by kalanir
  2

• Update Variant Calling workflow

  #212 opened 7 months ago by Talishask
  1

• 02-quality-control: clarification for transfer data from AWS to local desktop

  #258 opened 7 months ago by youyaqi
  0

• 02-quality-control: clarification for paired-end data

  #257 opened 7 months ago by youyaqi
  0

• Transition To Workbench in May

  #240 opened a year ago by zkamvar
  9

• for loop not saving unzipped files

  #250 opened a year ago by Luke-Zondagh
  1

• Variant Calling testing cmds should match script

  #247 opened a year ago by sstevens2
  0

• AWS AMI missing fastqc and related tools

  #209 opened 5 years ago by tejashree1modak
  1

• Shell scripting not effectively handled

  #174 opened 6 years ago by sstevens2
  4

• Update software versions

  #246 opened 2 years ago by bkmgit
  0

• Links need to be fixed in CONTRIBUTING.md

  #243 opened 2 years ago by tobyhodges
  0

• wrangling-genomics/04-variant_calling: download of fastq should have a download-free option

  #164 opened 6 years ago by JasonJWilliamsNY
  1

• Grammatical / typo errors in Trimming and Filtering

  #237 opened 2 years ago by anniewest
  0

• Add alt text for images included in the lesson for improved accessibility

  #236 opened 2 years ago by mellamosummer
  0

• Assessing Read Quality: Improve the visualisation of Phred Quality Scores

  #220 opened 4 years ago by theheking
  1

• Incorrect directory (bcf) under Step 3 in variant calling part

  #229 opened 3 years ago by waydeveldman
  2

• Need jump lists (anchors) for headings

  #230 opened 3 years ago by annajiat
  0

• Lesson Contribution: Assessing Read Quality

  #224 opened 4 years ago by Talishask
  1

• Error on scp with zsh

  #216 opened 3 years ago by ErinBecker
  1

• Where does the build recipe for the 'dataCgen-qc' AMI live?

  #221 opened 4 years ago by willfurnass
  0

• Adapt trimmomatic command

  #219 opened 4 years ago by larahurban
  0

• I have a problem with executing variant call

  #188 opened 5 years ago by otienolwanga
  7

• Use of SRA Explorer to Download FastQC Files ?

  #217 opened 4 years ago by jcjimbo
  0

• Add the use of MultiQC to combine fastqc file in section 02-quality-control

  #213 opened 5 years ago by ggrimes
  0

• Variant Calling Workflow: example has incorrect samtool sort options and param

  #211 opened 5 years ago by msuhovec
  1

• mkdir -p explanation at first occurrence

  #205 opened 5 years ago by aschuerch
  1

• 04-variant-calling: samtools vs. bcftools typo

  #201 opened 5 years ago by hoytpr
  2

• Typo in wrangling genomics 02-quality-control

  #198 opened 5 years ago by hoytpr
  3

• move multi-line commands callout?

  #202 opened 5 years ago by aschuerch
  2

• SRR2584866_final_variants.vcf is missing "results" data

  #200 opened 5 years ago by hoytpr
  0

• wrangling-genomics/03-trimming trimmomatic loop clarification needed

  #181 opened 5 years ago by hoytpr
  1

• Use of touch in "Automating a Variant Calling Workflow" lesson in Data Wrangling and Processing for Genomics

  #197 opened 5 years ago by cpaisie
  0

• Description of boxplots in "Assessing Read Quality"

  #195 opened 5 years ago by fsvarn
  3

• topic for the repository

  #193 opened 5 years ago by dpshelio
  3

• wrangling-genomics/04-variant_calling: More problems with TVIEW

  #179 opened 5 years ago by hoytpr
  1

• Extracting count matrix form the BAM files

  #190 opened 5 years ago by otienolwanga
  2

• Fastqc issues [Submitted by email]

  #187 opened 5 years ago by ErinBecker
  3

• Wording of aligner choice in lesson 04-variant_calling

  #189 opened 5 years ago by JanaSperschneider
  1

• When was FASTQC installed?

  #185 opened 5 years ago by Starbuck85
  3

• wrangling-genomics/01-background: lack of clarity in "View the Metadata" section (omission)

  #182 opened 6 years ago by ousodaniel
  0

• wrangling-genomics/02-quality-control: scp command needs clarity

  #180 opened 6 years ago by hoytpr
  0

• wrangling-genomics/04-variant_calling: IGV output

  #167 opened 6 years ago by JasonJWilliamsNY
  1

• Challenge callout not rendering correctly

  #172 opened 6 years ago by sstevens2
  1

• Windows line endings in metadata CSV

  #169 opened 6 years ago by tobyhodges
  0

• Why import files from ENA

  #173 opened 6 years ago by JasonJWilliamsNY
  0

• Confusing Metadata Descriptions

  #168 opened 6 years ago by elizabethmcd
  0

• wrangling-genomics/04-variant_calling: example is not a valid command

  #165 opened 6 years ago by JasonJWilliamsNY
  0

• wrangling-genomics/04-variant_calling: problems with TVIEW?

  #166 opened 6 years ago by JasonJWilliamsNY
  0