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:
- Input: merged_transcriptomes.fasta.
- Runs TransDecoder to produce longest_transcripts.fasta
- (Runs both the LongOrfs and Predict parts together. Default settings except Long Orfs options: -m =20)
- Runs Busco on output.
Inputs
ID | Name | Description | Type |
---|---|---|---|
merged_transcriptomes.fasta | #main/merged_transcriptomes.fasta | n/a |
|
Steps
ID | Name | Description |
---|---|---|
1 | Text transformation | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy1 |
2 | TransDecoder | toolshed.g2.bx.psu.edu/repos/iuc/transdecoder/transdecoder/5.5.0+galaxy2 |
3 | Busco | toolshed.g2.bx.psu.edu/repos/iuc/busco/busco/5.5.0+galaxy0 |
Outputs
ID | Name | Description | Type |
---|---|---|---|
busco_sum | #main/busco_sum | n/a |
|
busco_table | #main/busco_table | n/a |
|
out_bed | #main/out_bed | n/a |
|
out_cds | #main/out_cds | n/a |
|
out_gff3 | #main/out_gff3 | n/a |
|
out_lo_cds | #main/out_lo_cds | n/a |
|
out_lo_pep | #main/out_lo_pep | n/a |
|
out_pep | #main/out_pep | n/a |
|
Version History
Version 1 (earliest) Created 8th May 2024 at 08:15 by Anna Syme
Initial commit
Frozen
Version-1
3372155
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Creators
Submitter
Tools
Citation
Silver, L., & Syme, A. (2024). Extract transcripts - TSI. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.879.1
Activity
Views: 1213 Downloads: 103 Runs: 0
Created: 8th May 2024 at 08:15
Last updated: 9th May 2024 at 05:08
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