Find transcripts - 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:

  • Run this workflow per tissue.
  • Inputs: masked_genome.fasta and the trimmed RNAseq reads (R1 and R2) from one type of tissue.
  • Index genome and align reads to genome with HISAT2, with default settings except for: Advanced options: spliced alignment options: specify options: Transcriptome assembly reporting: selected option: Report alignments tailored for transcript assemblers including StringTie (equivalent to -dta flag).
  • Runs samtools sort to sort bam by coordinate.
  • Runs StringTie to generate gtf from sorted bam.
  • Output: transcripts.gtf from a single tissue.


ID Name Description Type
Trimmed, merged R1 files #main/Trimmed, merged R1 files n/a
  • File
Trimmed, merged R2 files #main/Trimmed, merged R2 files n/a
  • File
genome.fasta (use masked if available) #main/genome.fasta (use masked if available) n/a
  • File


ID Name Description
3 Build genome index and align reads with HISAT2
4 StringTie


ID Name Description Type
hisat2_summary_file #main/hisat2_summary_file n/a
  • File
output_alignments #main/output_alignments n/a
  • File
output_gtf #main/output_gtf n/a
  • File

Version History

Version 1 (earliest) Created 8th May 2024 at 07:51 by Anna Syme

Initial commit

Frozen Version-1 49078a8
help Creators and Submitter
Silver, L., & Syme, A. (2024). Find transcripts - TSI. WorkflowHub.

Views: 216

Created: 8th May 2024 at 07:51

Last updated: 9th May 2024 at 05:04

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Total size: 304 KB
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