trinity NG

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Workflow Type: Galaxy

roscoff hackathon

Associated Tutorial

This workflows is part of the tutorial trinity NG, available in the GTN

Thanks to...

Tutorial Author(s): Anthony Bretaudeau, Gildas Le Corguillé, Erwan Corre, Xi Liu

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1306?version=2

Inputs

ID Name Description Type
Collection of R1 reads Collection of R1 reads n/a
  • File[]
Collection of R2 reads Collection of R2 reads n/a
  • File[]
Samples description Samples description The list of samples and replicates. Can be created with the 'Describe samples and replicates' tool
  • File

Steps

ID Name Description
20 Trinotate toolshed.g2.bx.psu.edu/repos/iuc/trinotate/trinotate/3.1.1
21 Differential expression analysis toolshed.g2.bx.psu.edu/repos/iuc/trinity_run_de_analysis/trinity_run_de_analysis/2.8.4
22 Extract and cluster differentially expressed transcripts toolshed.g2.bx.psu.edu/repos/iuc/trinity_analyze_diff_expr/trinity_analyze_diff_expr/2.8.4
23 Partition genes into expression clusters toolshed.g2.bx.psu.edu/repos/iuc/trinity_define_clusters_by_cutting_tree/trinity_define_clusters_by_cutting_tree/2.8.4
2 Describe samples toolshed.g2.bx.psu.edu/repos/iuc/describe_samples/describe_samples/2.8.4
5 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69
4 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69
7 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.2.0
6 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.32.3
9 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69
8 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.69
11 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.2.0
10 Trinity toolshed.g2.bx.psu.edu/repos/iuc/trinity/trinity/2.8.4
13 Build expression matrix toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.4
12 Align reads and estimate abundance toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance/2.8.4
15 Filter low expression transcripts toolshed.g2.bx.psu.edu/repos/iuc/trinity_filter_low_expr_transcripts/trinity_filter_low_expr_transcripts/2.8.4
14 RNASeq samples quality check toolshed.g2.bx.psu.edu/repos/iuc/trinity_samples_qccheck/trinity_samples_qccheck/2.8.4
17 Align reads and estimate abundance toolshed.g2.bx.psu.edu/repos/iuc/trinity_align_and_estimate_abundance/trinity_align_and_estimate_abundance/2.8.4
16 Compute contig Ex90N50 statistic and Ex90 transcript count toolshed.g2.bx.psu.edu/repos/iuc/trinity_contig_exn50_statistic/trinity_contig_exn50_statistic/2.8.4
19 Build expression matrix toolshed.g2.bx.psu.edu/repos/iuc/trinity_abundance_estimates_to_matrix/trinity_abundance_estimates_to_matrix/2.8.4
18 TransDecoder toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/3.0.1

Outputs

ID Name Description Type
_anonymous_output_1 _anonymous_output_1 n/a
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File
_anonymous_output_3 _anonymous_output_3 n/a
  • File
_anonymous_output_4 _anonymous_output_4 n/a
  • File
_anonymous_output_5 _anonymous_output_5 n/a
  • File
_anonymous_output_6 _anonymous_output_6 n/a
  • File
_anonymous_output_7 _anonymous_output_7 n/a
  • File
_anonymous_output_11 _anonymous_output_11 n/a
  • File
_anonymous_output_12 _anonymous_output_12 n/a
  • File
_anonymous_output_13 _anonymous_output_13 n/a
  • File
_anonymous_output_14 _anonymous_output_14 n/a
  • File
_anonymous_output_15 _anonymous_output_15 n/a
  • File
_anonymous_output_16 _anonymous_output_16 n/a
  • File

Version History

1.0 (latest) Created 16th Jul 2024 at 14:05 by Helena Rasche

Added/updated 4 files


Open master caa24a6

2.0 (earliest) Created 25th Jun 2024 at 11:22 by Helena Rasche

Added/updated 4 files


Frozen 2.0 7c61af1
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
Trinotate
Trinity
FastQC
MultiQC
Trimmomatic
TransDecoder
License
Creative Commons Attribution 4.0 International
Activity

Views: 198   Downloads: 83

Created: 25th Jun 2024 at 11:22

Last updated: 25th Jun 2024 at 11:22

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