QC + Mapping + Counting (single+paired) - Ref Based RNA Seq - Transcriptomics - GTN

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Workflow Type: Galaxy

Reference-based RNA-Seq data analysis

Associated Tutorial

This workflows is part of the tutorial Reference-based RNA-Seq data analysis, available in the GTN

Features

Thanks to...

Workflow Author(s): Bérénice Batut, Mallory Freeberg, Mo Heydarian, Anika Erxleben, Pavankumar Videm, Clemens Blank, Maria Doyle, Nicola Soranzo, Peter van Heusden, Lucille Delisle

Tutorial Author(s): Bérénice Batut, Mallory Freeberg, Mo Heydarian, Anika Erxleben, Pavankumar Videm, Clemens Blank, Maria Doyle, Nicola Soranzo, Peter van Heusden, Lucille Delisle

Tutorial Contributor(s): Helena Rasche, Clea Siguret

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1329?version=4

Inputs

ID Name Description Type
Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz Drosophila_melanogaster.BDGP6.32.109_UCSC.gtf.gz n/a
  • File
paired fastqs paired fastqs n/a
  • File[]
single fastqs single fastqs n/a
  • File[]

Steps

ID Name Description
3 Cutadapt: remove bad quality bp toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1
4 Flatten paired collection for FastQC __FLATTEN__
5 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.9+galaxy1
6 Get gene length toolshed.g2.bx.psu.edu/repos/iuc/length_and_gc_content/length_and_gc_content/0.1.2
7 convert gtf to bed12 toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357
8 STAR: map single reads toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0
9 Merge fastqs for FastQC __MERGE_COLLECTION__
10 Merge Cutadapt reports __MERGE_COLLECTION__
11 STAR: map paired reads toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.11a+galaxy0
12 count reads per gene for SR toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2
13 FastQC check read qualities toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
14 Combine cutadapt results toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
15 Merge STAR logs __MERGE_COLLECTION__
16 Merge STAR counts __MERGE_COLLECTION__
17 count fragments per gene for PE toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy2
18 Merge STAR BAM __MERGE_COLLECTION__
19 merge coverage unique strand 1 __MERGE_COLLECTION__
20 merge coverage unique strand 2 __MERGE_COLLECTION__
21 Combine FastQC results toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
22 Combine STAR Results toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
23 Remove statistics from STAR counts toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_tail_tool/9.3+galaxy1
24 Determine library strandness with STAR toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
25 merge counts from featureCounts __MERGE_COLLECTION__
26 merge featureCounts summary __MERGE_COLLECTION__
27 Determine library strandness with Infer Experiment toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_infer_experiment/5.0.3+galaxy0
28 Read Distribution toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0
29 Compute read distribution statistics toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.3+galaxy0
30 sample BAM toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy2
31 Get reads number per chromosome toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.5
32 Remove duplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/3.1.1.0
33 Determine library strandness with STAR coverage toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy2
34 Select unstranded counts Cut1
35 Sort counts to get gene with highest count on feature Counts toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1
36 Combine read asignments statistics toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
37 Combine read distribution on known features toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
38 Get gene body coverage toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_geneBody_coverage/5.0.3+galaxy0
39 Combine results on reads per chromosome toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
40 Combine results of duplicate reads toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
41 Sort counts to get gene with highest count on STAR toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sort_header_tool/9.3+galaxy1
42 Combine gene body coverage toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1

Outputs

ID Name Description Type
Gene length Gene length n/a
  • File
_anonymous_output_1 _anonymous_output_1 n/a
  • File
multiqc_cutadapt_html multiqc_cutadapt_html n/a
  • File
featureCounts_gene_length featureCounts_gene_length n/a
  • File
STAR_BAM STAR_BAM n/a
  • File
multiqc_fastqc_html multiqc_fastqc_html n/a
  • File
multiqc_star_html multiqc_star_html n/a
  • File
multiqc_star_counts_html multiqc_star_counts_html n/a
  • File
featureCounts featureCounts n/a
  • File
inferexperiment inferexperiment n/a
  • File
_anonymous_output_2 _anonymous_output_2 n/a
  • File
_anonymous_output_3 _anonymous_output_3 n/a
  • File
pgt pgt n/a
  • File
counts_from_star counts_from_star n/a
  • File
featureCounts_sorted featureCounts_sorted n/a
  • File
multiqc_featureCounts_html multiqc_featureCounts_html n/a
  • File
multiqc_read_distrib multiqc_read_distrib n/a
  • File
multiqc_reads_per_chrom multiqc_reads_per_chrom n/a
  • File
multiqc_dup multiqc_dup n/a
  • File
counts_from_star_sorted counts_from_star_sorted n/a
  • File
multiqc_gene_body_cov multiqc_gene_body_cov n/a
  • File

Version History

5.0 (latest) Created 28th Oct 2024 at 13:08 by Helena Rasche

Added/updated 4 files


Open master 0215b59

4.0 Created 16th Jul 2024 at 14:05 by Helena Rasche

Added/updated 4 files


Frozen 4.0 66ea6b7

9.0 Created 5th Jul 2024 at 14:24 by Helena Rasche

Added/updated 4 files


Frozen 9.0 b72a251

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

Added/updated 4 files


Frozen 7.0 aa7015d
help Creators and Submitter
Creators
Not specified
Submitter
Discussion Channel
GTN Matrix
Tools
Cutadapt
R
STAR
FeatureCounts
FastQC
MultiQC
RSeQC
SAMtools
pyGenomeTracks
License
MIT License
Activity

Views: 626   Downloads: 236

Created: 25th Jun 2024 at 11:25

Last updated: 28th Oct 2024 at 13:08

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