datacarpentry wrangling-genomics issues

datacarpentry / wrangling-genomics

Data Wrangling and Processing for Genomics

https://datacarpentry.org/wrangling-genomics/

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Update Variant Calling workflow

#212 Talishask closed 4 months ago
1
Variant Calling Workflow: example has incorrect samtool sort options and param

#211 msuhovec opened 4 years ago
1
Adding a sanity check for fastqc being installed

#210 tejashree1modak closed 4 years ago
3
AWS AMI missing fastqc and related tools

#209 tejashree1modak opened 4 years ago
1
removal of mac 'open' command (issue 126)

#208 swbioinf closed 4 years ago
3
path typo in fastq text episode 05

#207 hoytpr closed 4 years ago
1
moved explanation of mkdir -p to first occurrence

#206 aschuerch closed 4 years ago
1
mkdir -p explanation at first occurrence

#205 aschuerch closed 4 years ago
1
typos in episodes 04 and 02

#204 hoytpr closed 4 years ago
1
moving multi-line callout

#203 aschuerch closed 4 years ago
1
move multi-line commands callout?

#202 aschuerch closed 4 years ago
2
04-variant-calling: samtools vs. bcftools typo

#201 hoytpr closed 4 years ago
2
SRR2584866_final_variants.vcf is missing "results" data

#200 hoytpr opened 4 years ago
0
Modify workflow image

#199 biowizz closed 4 years ago
2
Typo in wrangling genomics 02-quality-control

#198 hoytpr closed 4 years ago
3
Use of touch in "Automating a Variant Calling Workflow" lesson in Data Wrangling and Processing for Genomics

#197 cpaisie opened 5 years ago
0
boxplot description update

#196 fsvarn closed 5 years ago
1
Description of boxplots in "Assessing Read Quality"

#195 fsvarn closed 5 years ago
3
Contribution for instructor checkout: Nooriyah

#194 nooriyahp closed 5 years ago
1
topic for the repository

#193 dpshelio closed 5 years ago
3
making quality coding consistent with reads

#192 laninsky closed 5 years ago
3
Added prompt to command that didn't have one

#191 laninsky closed 5 years ago
1
Extracting count matrix form the BAM files

#190 otienolwanga closed 5 years ago
2
Wording of aligner choice in lesson 04-variant_calling

#189 JanaSperschneider opened 5 years ago
1
I have a problem with executing variant call

#188 otienolwanga opened 5 years ago
7
Fastqc issues [Submitted by email]

#187 ErinBecker closed 5 years ago
3
Added links to FastQC documentation and added missing K-mer Content g…

#186 tkchafin closed 5 years ago
1
When was FASTQC installed?

#185 Starbuck85 closed 5 years ago
3
Fixed typos/punctuation

#184 BinxiePeterson closed 5 years ago
1
Update 04-variant_calling.md

#183 murraycadzow closed 5 years ago
1
wrangling-genomics/01-background: lack of clarity in "View the Metadata" section (omission)

#182 ousodaniel opened 5 years ago
0
wrangling-genomics/03-trimming trimmomatic loop clarification needed

#181 hoytpr closed 4 years ago
1
wrangling-genomics/02-quality-control: scp command needs clarity

#180 hoytpr opened 5 years ago
0
wrangling-genomics/04-variant_calling: More problems with TVIEW

#179 hoytpr closed 5 years ago
1
fix odd link

#178 ErinBecker closed 5 years ago
1
Format challenge

#177 ErinBecker closed 5 years ago
1
Remove dcuser password

#176 ErinBecker closed 5 years ago
1
Correction of typos/errors in wrangling materials

#175 mfernandes61 closed 5 years ago
2
Shell scripting not effectively handled

#174 sstevens2 opened 5 years ago
4
Why import files from ENA

#173 JasonJWilliamsNY opened 5 years ago
0
Challenge callout not rendering correctly

#172 sstevens2 opened 5 years ago
1
Change line endings

#171 tobyhodges closed 5 years ago
1
use remote theme

#170 fmichonneau closed 5 years ago
0
Windows line endings in metadata CSV

#169 tobyhodges closed 5 years ago
0
Confusing Metadata Descriptions

#168 elizabethmcd opened 5 years ago
0
wrangling-genomics/04-variant_calling: IGV output

#167 JasonJWilliamsNY opened 5 years ago
1
wrangling-genomics/04-variant_calling: problems with TVIEW?

#166 JasonJWilliamsNY opened 5 years ago
0
wrangling-genomics/04-variant_calling: example is not a valid command

#165 JasonJWilliamsNY opened 5 years ago
0
wrangling-genomics/04-variant_calling: download of fastq should have a download-free option

#164 JasonJWilliamsNY opened 5 years ago
1
wrangling-genomics/04-variant_calling: download of bacterial ref genome should talk about checksums

#163 JasonJWilliamsNY opened 5 years ago
0

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