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 QC + Mapping + Counting (single+paired) - Ref Based RNA Seq - Transcriptomics - GTN, available in the GTN

Features

Thanks to...

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

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

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1329?version=1

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/4.0+galaxy1
4 Flatten paired collection for FastQC __FLATTEN__
5 Cutadapt toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+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/2.7.10b+galaxy3
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/2.7.10b+galaxy3
12 count reads per gene for SR toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/2.0.3+galaxy1
13 FastQC check read qualities toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.73+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+galaxy1
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/1.1.0
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/5.0.1+galaxy2
28 Read Distribution toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.1+galaxy2
29 Compute read distribution statistics toolshed.g2.bx.psu.edu/repos/nilesh/rseqc/rseqc_read_distribution/5.0.1+galaxy2
30 sample BAM toolshed.g2.bx.psu.edu/repos/iuc/samtools_view/samtools_view/1.15.1+galaxy0
31 Get reads number per chromosome toolshed.g2.bx.psu.edu/repos/devteam/samtools_idxstats/samtools_idxstats/2.0.4
32 Remove duplicates toolshed.g2.bx.psu.edu/repos/devteam/picard/picard_MarkDuplicates/2.18.2.4
33 Determine library strandness with STAR coverage toolshed.g2.bx.psu.edu/repos/iuc/pygenometracks/pygenomeTracks/3.8+galaxy1
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/1.1.1
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/5.0.1+galaxy2
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/1.1.1
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: 635   Downloads: 245

Created: 25th Jun 2024 at 11:25

Last updated: 28th Oct 2024 at 13:08

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