Workflow Type: Galaxy
Frozen
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.
Inputs
ID | Name | Description | Type |
---|---|---|---|
Trimmed, merged R1 files | #main/Trimmed, merged R1 files | n/a |
|
Trimmed, merged R2 files | #main/Trimmed, merged R2 files | n/a |
|
genome.fasta (use masked if available) | #main/genome.fasta (use masked if available) | n/a |
|
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 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
hisat2_summary_file | #main/hisat2_summary_file | n/a |
|
output_alignments | #main/output_alignments | n/a |
|
output_gtf | #main/output_gtf | n/a |
|
Version History
Version 1 (earliest) Created 8th May 2024 at 07:51 by Anna Syme
Initial commit
Frozen
Version-1
49078a8
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Creators
Submitter
Citation
Silver, L., & Syme, A. (2024). Find transcripts - TSI. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.877.1
Activity
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Created: 8th May 2024 at 07:51
Last updated: 9th May 2024 at 05:04
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