Plant bulk RNA-Seq workflow

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Workflow Type: Galaxy

Identify upregulated miRNAS and analyze potential targets in downregulated genes.

Associated Tutorial

This workflows is part of the tutorial Plant bulk RNA-Seq workflow, available in the GTN

Thanks to...

Tutorial Author(s): Cristóbal Gallardo, Pavankumar Videm, Beatriz Serrano-Solano

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1318?version=2

Inputs

ID Name Description Type
Annotation GTF #main/Annotation GTF n/a
  • File
Control mRNA FASTQ collection #main/Control mRNA FASTQ collection n/a
  • array containing
    • File
Control miRNA FASTQ collection #main/Control miRNA FASTQ collection n/a
  • array containing
    • File
Mature miRNA sequences #main/Mature miRNA sequences n/a
  • File
Precursor miRNA sequences #main/Precursor miRNA sequences n/a
  • File
Star miRNA sequenes #main/Star miRNA sequenes n/a
  • File
Transcriptome FASTA #main/Transcriptome FASTA n/a
  • File
Treated mRNA FASTQ collection #main/Treated mRNA FASTQ collection n/a
  • array containing
    • File
Treated miRNA FASTQ collection #main/Treated miRNA FASTQ collection n/a
  • array containing
    • File

Steps

ID Name Description
9 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
10 Trim Galore! toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1
11 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
12 Trim Galore! toolshed.g2.bx.psu.edu/repos/bgruening/trim_galore/trim_galore/0.4.3.1
13 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
14 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
15 Salmon quant toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1.2+galaxy1
16 Salmon quant toolshed.g2.bx.psu.edu/repos/bgruening/salmon/salmon/0.14.1.2+galaxy1
17 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
18 MiRDeep2 Mapper toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper/2.0.0
19 Merge collections __MERGE_COLLECTION__
20 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.72+galaxy1
21 MiRDeep2 Mapper toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_mapper/rbc_mirdeep2_mapper/2.0.0
22 Merge collections __MERGE_COLLECTION__
23 DESeq2 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1
24 MiRDeep2 Quantifier toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0
25 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7
26 Merge collections __MERGE_COLLECTION__
27 MiRDeep2 Quantifier toolshed.g2.bx.psu.edu/repos/rnateam/mirdeep2_quantifier/rbc_mirdeep2_quantifier/2.0.0
28 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7
29 Filter Filter1
30 Cut Cut1
31 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.7
32 Cut Cut1
33 Filter Filter1
34 Filter Filter1
35 DESeq2 toolshed.g2.bx.psu.edu/repos/iuc/deseq2/deseq2/2.11.40.6+galaxy1
36 Cut Cut1
37 Filter Filter1
38 Filter FASTA toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1
39 Filter Filter1
40 Filter Filter1
41 Cut Cut1
42 Filter FASTA toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1
43 Filter FASTA toolshed.g2.bx.psu.edu/repos/galaxyp/filter_by_fasta_ids/filter_by_fasta_ids/2.1
44 Concatenate datasets cat1
45 TargetFinder toolshed.g2.bx.psu.edu/repos/rnateam/targetfinder/targetfinder/1.7.0+galaxy1

Outputs

ID Name Description Type
_anonymous_output_1 #main/_anonymous_output_1 n/a
  • File
_anonymous_output_10 #main/_anonymous_output_10 n/a
  • File
_anonymous_output_2 #main/_anonymous_output_2 n/a
  • File
_anonymous_output_3 #main/_anonymous_output_3 n/a
  • File
_anonymous_output_4 #main/_anonymous_output_4 n/a
  • File
_anonymous_output_5 #main/_anonymous_output_5 n/a
  • File
_anonymous_output_6 #main/_anonymous_output_6 n/a
  • File
_anonymous_output_7 #main/_anonymous_output_7 n/a
  • File
_anonymous_output_8 #main/_anonymous_output_8 n/a
  • File
_anonymous_output_9 #main/_anonymous_output_9 n/a
  • File

Version History

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

Added/updated 4 files


Open master dd404d0

7.0 (earliest) Created 25th Jun 2024 at 11:23 by Helena Rasche

Added/updated 4 files


Frozen 7.0 688933e
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
FastQC
Trim Galore
Salmon
miRDeep2
DESeq2
MultiQC
Targetfinder.org
License
Creative Commons Attribution 4.0 International
Activity

Views: 493   Downloads: 148

Created: 25th Jun 2024 at 11:23

Last updated: 25th Jun 2024 at 11:23

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