rnaseq-pe/main

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Workflow Type: Galaxy

This workflow takes as input a list of paired-end fastqs. Adapters and bad quality bases are removed with cutadapt. Reads are mapped with STAR with ENCODE parameters and genes are counted simultaneously. The counts are reprocess to be similar to HTSeq-count output. FPKM are computed with cufflinks. Coverage (per million mapped reads) are computed with bedtools on uniquely mapped reads (with R2 orientation inverted).

SEEK ID: https://workflowhub.eu/workflows/401?version=5

Inputs

ID Name Description Type
PE fastq input PE fastq input Should be a list of paired-end RNA-seq fastqs
  • File[]
forward_adapter forward_adapter Please use: For R1: - For Nextera: CTGTCTCTTATACACATCTCCGAGCCCACGAGAC - For TrueSeq: GATCGGAAGAGCACACGTCTGAACTCCAGTCAC or AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC
  • string
gtf gtf gtf compatible with the reference_genome. Mind the UCSC/Ensembl differences in chromosome naming
  • File
gtf with regions to exclude from FPKM normalization gtf with regions to exclude from FPKM normalization Could be a gtf with for example one entry for the chrM forward and one entry for the chrM reverse
  • File?
reference_genome reference_genome reference_genome
  • string
reverse_adapter reverse_adapter Please use: For R2: - For Nextera: CTGTCTCTTATACACATCTGACGCTGCCGACGA - For TruSeq: GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT or AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGT
  • string
strandness strandness For stranded RNA, reverse means that the read is complementary to the coding sequence, forward means that the read is in the same orientation as the coding sequence
  • string

Steps

ID Name Description
7 Cutadapt (remove adapter + bad quality bases) toolshed.g2.bx.psu.edu/repos/lparsons/cutadapt/cutadapt/4.0+galaxy1
8 get reference_genome as text parameter toolshed.g2.bx.psu.edu/repos/iuc/compose_text_param/compose_text_param/0.1.1
9 awk command from strand toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1
10 bedtools orientation for forward coverage toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1
11 bedtools orientation for reverse coverage toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1
12 Get cufflinks strandess parameter toolshed.g2.bx.psu.edu/repos/iuc/map_param_value/map_param_value/0.1.1
13 STAR: map and count toolshed.g2.bx.psu.edu/repos/iuc/rgrnastar/rna_star/2.7.8a+galaxy1
14 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
15 Extract gene counts toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
16 Keep only uniquely mapped reads toolshed.g2.bx.psu.edu/repos/devteam/bamtools_filter/bamFilter/2.5.2+galaxy1
17 get scaling factor This step get 1 / millions of uniquely mapped reads toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/1.1.2
18 Compute FPKM toolshed.g2.bx.psu.edu/repos/devteam/cufflinks/cufflinks/2.2.1.3
19 revertR2orientationInBam toolshed.g2.bx.psu.edu/repos/lldelisle/revertr2orientationinbam/revertR2orientationInBam/0.0.2
20 convert dataset to parameter param_value_from_file
21 Scaled Coverage both strands combined toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0
22 Scaled Coverage positive toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0
23 Scaled Coverage negative toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_genomecoveragebed/2.30.0
24 convert both strands coverage to bigwig wig_to_bigWig
25 convert positive coverage to bigwig wig_to_bigWig
26 convert negative coverage to bigwig wig_to_bigWig

Outputs

ID Name Description Type
mapped-reads mapped-reads n/a
  • File
output_log output_log n/a
  • File
reads_per_gene from STAR reads_per_gene from STAR n/a
  • File
MultiQC webpage MultiQC webpage n/a
  • File
MultiQC on input dataset(s): Stats MultiQC on input dataset(s): Stats n/a
  • File
HTS count like output HTS count like output n/a
  • File
genes_expression genes_expression n/a
  • File
transcripts_expression transcripts_expression n/a
  • File
both strands coverage both strands coverage n/a
  • File
positive strand coverage positive strand coverage n/a
  • File
negative strand coverage negative strand coverage n/a
  • File

Version History

v0.9 (latest) Created 7th Oct 2024 at 16:33 by WorkflowHub Bot

Updated to v0.9


Frozen v0.9 5b0324e

v0.6 Created 7th Oct 2024 at 16:33 by WorkflowHub Bot

Updated to v0.6


Frozen v0.6 a7e0a3d

v0.8 Created 16th Jul 2024 at 03:03 by WorkflowHub Bot

Updated to v0.8


Frozen v0.8 bbbad57

v0.7 Created 29th Jun 2024 at 03:02 by WorkflowHub Bot

Updated to v0.7


Frozen v0.7 ddf092f

v0.5 Created 16th Sep 2023 at 03:01 by WorkflowHub Bot

Updated to v0.5


Frozen v0.5 93a3560

v0.4.1 Created 15th Sep 2023 at 03:01 by WorkflowHub Bot

Updated to v0.4.1


Frozen v0.4.1 7acbe8e

v0.4 Created 17th Jan 2023 at 03:01 by WorkflowHub Bot

Updated to v0.4


Frozen v0.4 387b362

v0.3 Created 14th Jan 2023 at 03:01 by WorkflowHub Bot

Updated to v0.3


Frozen v0.3 a0b796b

v0.2 Created 1st Dec 2022 at 03:01 by WorkflowHub Bot

Updated to v0.2


Frozen v0.2 61f6547

v0.1 (earliest) Created 25th Oct 2022 at 03:01 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 4c67dcd
help Creators and Submitter
Creator
  • Lucille Delisle
Additional credit

Lucille Delisle

Submitter
Tools
Cutadapt
STAR
MultiQC
Cufflinks
License
MIT License
Activity

Views: 5306   Downloads: 1225   Runs: 1

Created: 25th Oct 2022 at 03:01

Last updated: 17th Jan 2023 at 03:01

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