trinity NG

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

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

trinity NG
2.0 (earliest)

1.0 (latest)

2.0 (earliest)

Associated Tutorial

Thanks to...

Inputs

Steps

Outputs

Version History

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

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

Creators

Submitter

trinity NG 2.0 (earliest) 1.0 (latest) 2.0 (earliest)

Associated Tutorial

Thanks to...

Inputs

Steps

Outputs

Version History

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

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

Creators

Submitter

Related items

trinity NG
2.0 (earliest)

1.0 (latest)

2.0 (earliest)