Workflow Type: Galaxy
Open
Frozen
RAD-Seq Reference-based data analysis
Associated Tutorial
This workflows is part of the tutorial Workflow Constructed From History 'STACKS RAD: Population Genomics With Reference Genome', available in the GTN
Thanks to...
Tutorial Author(s): Yvan Le Bras
Inputs
ID | Name | Description | Type |
---|---|---|---|
SRR034310.fastq.gz | EBI SRA: SRR034310 File: ftp://ftp.sra.ebi.ac.uk/vol1/fastq/SRR034/SRR034310/SRR034310.fastq.gz | n/a |
|
Barcode_SRR034310.txt | https://zenodo.org/record/1134547/files/Barcode_SRR034310.txt | n/a |
|
Details_Barcode_Population_SRR034310.txt | https://zenodo.org/record/1134547/files/Details_Barcode_Population_SRR034310.txt | n/a |
|
Reference_genome_11_chromosomes.fasta | https://zenodo.org/record/1134547/files/Reference_genome_11_chromosomes.fasta | n/a |
|
Steps
ID | Name | Description |
---|---|---|
10 | FastQC | toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.71 |
11 | Map with BWA | toolshed.g2.bx.psu.edu/repos/devteam/bwa/bwa/0.7.17.4 |
12 | Select | Grep1 |
13 | Select | Grep1 |
14 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1 |
15 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1 |
16 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1 |
17 | MultiQC | toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.6 |
18 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1 |
19 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1 |
20 | Add column | addValue |
21 | Concatenate datasets | cat1 |
22 | Cut | Cut1 |
23 | Convert | Convert characters1 |
24 | Regex Replace | toolshed.g2.bx.psu.edu/repos/kellrott/regex_replace/regex_replace/1.0.0 |
25 | Stacks: reference map | toolshed.g2.bx.psu.edu/repos/iuc/stacks_refmap/stacks_refmap/1.46.0 |
26 | Stacks: populations | toolshed.g2.bx.psu.edu/repos/iuc/stacks_populations/stacks_populations/1.46.0 |
27 | Summary Statistics | Summary_Statistics1 |
28 | Sort | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/1.1.1 |
29 | Count | Count1 |
30 | Filter | Filter1 |
4 | Stacks: process radtags | toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0 |
5 | Stacks: process radtags | toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0 |
6 | Stacks: process radtags | toolshed.g2.bx.psu.edu/repos/iuc/stacks_procrad/stacks_procrad/1.46.0 |
7 | Replace Text | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/1.1.1 |
8 | Select | Grep1 |
9 | Select | Grep1 |
Version History
3.0 (latest) Created 16th Jul 2024 at 14:10 by Helena Rasche
Added/updated 4 files
Open
master
fd50aee
5.0 (earliest) Created 25th Jun 2024 at 11:15 by Helena Rasche
Added/updated 4 files
Frozen
5.0
a6c37f4
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
Creators
Not specifiedSubmitter
Discussion Channel
Activity
Views: 170 Downloads: 71
Created: 25th Jun 2024 at 11:15
Last updated: 25th Jun 2024 at 11:15
![help](/assets/famfamfam_silk/information-8cfe563be76fb11b27c8ba778f5d40ce6800b244d6ca58ef6e9973308efbe534.png)
None