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.

SEEK ID: https://workflowhub.eu/workflows/877?version=1

DOI: 10.48546/workflowhub.workflow.877.1

Inputs

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

Steps

ID	Name	Description
3	Build genome index and align reads with HISAT2	toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.2.1+galaxy1
4	StringTie	toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie/2.2.1+galaxy1