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

Includes Galaxy Workflow Tests

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, Wolfgang Maier, Pavankumar Videm, Bérénice Batut, Lucille Delisle, Björn Grüning, Nicola Soranzo, Hans-Rudolf Hotz, Cristóbal Gallardo, Saskia Hiltemann, Graeme Tyson, Maria Doyle, Amirhossein Naghsh Nilchi, Mehmet Tekman, Anika Erxleben, Simon Bray, Clemens Blank, Ekaterina Polkh, William Durand, Marius van den Beek, Niall Beard

SEEK ID: https://dev.workflowhub.eu/workflows/1329?version=5

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 Falco	__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 Falco	__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	Falco	toolshed.g2.bx.psu.edu/repos/iuc/falco/falco/1.2.4+galaxy0
14	Combine cutadapt results	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0
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/1.24.1+galaxy0
22	Combine STAR Results	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0
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/1.24.1+galaxy0
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/1.24.1+galaxy0
37	Combine read distribution on known features	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0
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/1.24.1+galaxy0
40	Combine results of duplicate reads	toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.24.1+galaxy0
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/1.24.1+galaxy0

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_falco_html	multiqc_falco_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