GTN_differential_isoform_expression

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Workflow Type: Galaxy

Training workflow

Associated Tutorial

This workflows is part of the tutorial Genome-wide alternative splicing analysis: human, available in the GTN

Features

Thanks to...

Tutorial Author(s): Cristóbal Gallardo, Lucille Delisle

Tutorial Contributor(s): Pavankumar Videm

Workflow Author(s): Cristóbal Gallardo Alba

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1324?version=1

Inputs

ID Name Description Type
Active sites dataset Active sites dataset Active sites dataset.
  • File
CPAT header CPAT header Galaxy compatible CPAT header.
  • File
Control IDs Control IDs IDs of control sequences, corresponding to filenames.
  • File
Factor 01 Factor 01 First factor name.
  • string
Factor 02 Factor 02 Second factor name.
  • string
Genome annotation Genome annotation Reference genome annotation in GTF format.
  • File
Pfam-A HMM Stockholm file Pfam-A HMM Stockholm file Stockholm file.
  • File
Pfam-A HMM library Pfam-A HMM library HMM library.
  • File
RNA-seq data collection RNA-seq data collection Collection of paired-end RNA-seq datasets.
  • File[]
Reference genome Reference genome Genome reference in FASTA format.
  • File

Steps

ID Name Description
10 fastp toolshed.g2.bx.psu.edu/repos/iuc/fastp/fastp/0.23.2+galaxy0
11 Flatten collection __FLATTEN__
12 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
13 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
14 Convert GTF to BED12 toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357
15 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+galaxy0
16 gffread toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0
17 gffread toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0
18 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
19 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
20 Concatenate datasets toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1
21 Search in textfiles toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_grep_tool/1.1.1
22 Cut Cut1
23 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
24 Parse parameter value param_value_from_file
25 RNA STAR toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3
26 Concatenate datasets toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1
27 Text reformatting ($5 > 0 && $7 > 3 && $6==0) toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
28 Cut Cut1
29 Sort sort1
30 Unique toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sorted_uniq/1.1.0
31 RNA STAR toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.10b+galaxy3
32 StringTie toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.1+galaxy1
33 Junction Annotation toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_annotation/5.0.1+galaxy2
34 Junction Saturation toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_junction_saturation/5.0.1+galaxy2
35 Gene Body Coverage (BAM) toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.1+galaxy2
36 Inner Distance toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_inner_distance/5.0.1+galaxy2
37 Infer Experiment toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/5.0.1+galaxy2
38 Read Distribution toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.1+galaxy2
39 gffread toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0
40 StringTie merge toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.1+galaxy1
41 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
42 rnaQUAST toolshed.g2.bx.psu.edu/repos/iuc/rnaquast/rna_quast/2.2.3+galaxy0
43 gffread toolshed.g2.bx.psu.edu/repos/devteam/gffread/gffread/2.2.1.3+galaxy0
44 StringTie toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.1+galaxy1
45 Filter collection __FILTER_FROM_FILE__
46 IsoformSwitchAnalyzeR toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5
47 IsoformSwitchAnalyzeR toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5
48 CPAT toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/3.0.4+galaxy0
49 PfamScan toolshed.g2.bx.psu.edu/repos/bgruening/pfamscan/pfamscan/1.6+galaxy0
50 Remove beginning Remove beginning1
51 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
52 Concatenate datasets toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1
53 IsoformSwitchAnalyzeR toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5
54 IsoformSwitchAnalyzeR toolshed.g2.bx.psu.edu/repos/iuc/isoformswitchanalyzer/isoformswitchanalyzer/1.20.0+galaxy5

Outputs

ID Name Description Type
lncRNA sequences lncRNA sequences n/a
  • File
protein coding sequences protein coding sequences n/a
  • File

Version History

3.0 (latest) Created 16th Sep 2024 at 14:07 by Helena Rasche

Added/updated 4 files


Open master 1b3f813

2.0 Created 16th Jul 2024 at 14:06 by Helena Rasche

Added/updated 4 files


Frozen 2.0 3acb26d

14.0 (earliest) Created 25th Jun 2024 at 11:24 by Helena Rasche

Added/updated 4 files


Frozen 14.0 539ac6b
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
fastp
FastQC
gffread
MultiQC
STAR
StringTie
RSeQC
rnaQUAST
IsoformSwitchAnalyzeR
PfamScan
gffcompare
pyGenomeTracks
License
Creative Commons Attribution Share Alike 4.0 International
Activity

Views: 546   Downloads: 185

Created: 25th Jun 2024 at 11:24

Last updated: 16th Sep 2024 at 14:07

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