Combine transcripts - TSI Version 1
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Run on GalaxyThis 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:
- Inputs: multiple transcriptome.gtfs from different tissues, genome.fasta, coding_seqs.fasta, non_coding_seqs.fasta
- Runs StringTie merge to combine transcriptomes, with default settings except for -m = 30 and -F = 0.1, to produce a merged_transcriptomes.gtf.
- Runs Convert GTF to BED12 with default settings, to produce a merged_transcriptomes.bed.
- Runs bedtools getfasta with default settings except for -name = yes, -s = yes, -split - yes, to produce a merged_transcriptomes.fasta
- Runs CPAT to generate seqs with high coding probability.
- Filters out non-coding seqs from the merged_transcriptomes.fasta
- Output: filtered_merged_transcriptomes.fasta
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Collection of transcriptome.gtf files | #main/Collection of transcriptome.gtf files | n/a |
|
| coding_seqs.fasta | #main/coding_seqs.fasta | n/a |
|
| genome.fasta | #main/genome.fasta | n/a |
|
| non_coding_seqs.fasta | #main/non_coding_seqs.fasta | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | StringTie merge | toolshed.g2.bx.psu.edu/repos/iuc/stringtie/stringtie_merge/2.2.1+galaxy1 |
| 5 | Convert GTF to BED12 | toolshed.g2.bx.psu.edu/repos/iuc/gtftobed12/gtftobed12/357 |
| 6 | bedtools getfasta | toolshed.g2.bx.psu.edu/repos/iuc/bedtools/bedtools_getfastabed/2.30.0+galaxy1 |
| 7 | CPAT (check settings) | The table of best probabilities is called orf_seqs_prob_best; converted this to tabular toolshed.g2.bx.psu.edu/repos/bgruening/cpat/cpat/3.0.5+galaxy0 |
| 8 | Filter and keep only seqs with >0.5 coding prob | skipping 1 header line Filter1 |
| 9 | Keep only column 1 - read headers | toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_cut_tool/9.3+galaxy0 |
| 10 | Fix headers to overwrite some uppercase | part of the headers have become capitalized, this reverts everything after the :: to lowercase. May need to be changed if headers don't have the same format with a :: in them. toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_sed_tool/9.3+galaxy0 |
| 11 | Filter out non-coding seqs (check output) | toolshed.g2.bx.psu.edu/repos/peterjc/seq_filter_by_id/seq_filter_by_id/0.2.9 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| bed_file | #main/bed_file | n/a |
|
| no_orf_seqs | #main/no_orf_seqs | n/a |
|
| orf_seqs | #main/orf_seqs | n/a |
|
| orf_seqs_prob | #main/orf_seqs_prob | n/a |
|
| orf_seqs_prob_best | #main/orf_seqs_prob_best | n/a |
|
| out_file1 | #main/out_file1 | n/a |
|
| out_gtf | #main/out_gtf | n/a |
|
| output | #main/output | n/a |
|
| output_pos | #main/output_pos | n/a |
|
Version History
Version 1 (earliest) Created 8th May 2024 at 08:07 by Anna Syme
Initial commit
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Version-1ff43cfe
Views: 1567 Downloads: 126 Runs: 0
Created: 8th May 2024 at 08:07
Last updated: 9th May 2024 at 05:06
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https://orcid.org/0000-0002-9906-0673
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Teams: Australian BioCommons, QCIF Bioinformatics, Pawsey Supercomputing Research Centre, Sydney Informatics Hub, Janis, Melbourne Data Analytics Platform (MDAP), Galaxy Australia
Web page: https://www.biocommons.org.au/
The Australian BioCommons enhances digital life science research through world class collaborative distributed infrastructure. It aims to ensure that Australian life science research remains globally competitive, through sustained strategic leadership, research community engagement, digital service provision, training and support.
Space: Australian BioCommons
Public web page: https://www.biocommons.org.au/
Galaxy is an open, web-based platform for accessible, reproducible, and transparent computational biological research.
- Accessible: Users can easily run tools without writing code or using the CLI; all via a user-friendly web interface.
- Reproducible: Galaxy captures all the metadata from an analysis, making it completely reproducible.
- Transparent: Users share and publish analyses via interactive pages that can enhance analyses with user annotations.
- Scalable: Galaxy ...
Space: Australian BioCommons
Public web page: https://usegalaxy.org.au/
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
