QC and trimming of RNAseq reads - TSI
Version 1

Workflow Type: Galaxy

This is part of a series of workflows to annotate a genome, tagged with TSI-annotation. These workflows are based on command-line code by Luke Silver, converted into Galaxy Australia workflows.

The workflows can be run in this order:

  • Repeat masking
  • RNAseq QC and read trimming
  • Find transcripts
  • Combine transcripts
  • Extract transcripts
  • Convert formats
  • Fgenesh annotation

About this workflow:

  • Repeat this workflow separately for datasets from different tissues.
  • Inputs = collections of R1 files, and R2 files (all from a single tissue type).
  • Runs FastQC with default settings, separately for raw reads R1 and R2 collections; all output to MultiQC.
  • Runs Trimmomatic with initial ILLUMINACLIP step (using standard adapter sequence for TruSeq3 paired-ended), uses settings SLIDINGWINDOW:4:5 LEADING:5 TRAILING:5 MINLEN:25, retain paired (not unpaired) outputs. User can modify at runtime.
  • Runs FastQC with default settings, separately for trimmed R1 and R2 collections; all output to MultiQC.
  • From Trimmomatic output: concatenate all R1 reads; concatenate all R2 reads.
  • Outputs = trimmed merged R1 file, trimmed merged R2 file.
  • Log files from Trimmomatic to MultiQC, to summarise trimming results.
  • Note: a known bug with MultiQC html output is that plot is labelled as "R1" reads, when it actually contains information from both R1 and R2 read sets - this is under investigation (and is due to a Trimmomatic output file labelling issue).
  • MultiQC results table formatted to show % of reads retained after trimming, table included in workflow report.
  • Note: a known bug is that sometimes the workflow report text resets to default text. To restore, look for an earlier workflow version with correct workflow report text, and copy and paste report text into current version.


ID Name Description
2 FastQC on R1 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
3 FastQC on R2 toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
4 Trimmomatic toolshed.g2.bx.psu.edu/repos/pjbriggs/trimmomatic/trimmomatic/0.36.6
5 MultiQC on raw reads toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
6 MultiQC on trimmomatic logs toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
7 Merge all the R1 files toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1
8 Merge all the R2 files toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cat/0.1.1
9 Extract dataset __EXTRACT_DATASET__
10 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
11 FastQC toolshed.g2.bx.psu.edu/repos/devteam/fastqc/fastqc/0.74+galaxy0
12 Cut Cut1
13 MultiQC toolshed.g2.bx.psu.edu/repos/iuc/multiqc/multiqc/1.11+galaxy1
14 Remove beginning Remove beginning1
15 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/1.1.3

Version History

Version 1 (earliest) Created 8th May 2024 at 07:39 by Anna Syme

Initial commit

Frozen Version-1 0aa7186
help Creators and Submitter
Silver, L., & Syme, A. (2024). QC and trimming of RNAseq reads - TSI. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.876.1

Views: 208

Created: 8th May 2024 at 07:39

Last updated: 9th May 2024 at 05:02

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Total size: 2.08 MB
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