GigaScience-RNAseq-Optitype-seq2HLA-to-IEDB-alleles 1.0
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Run on GalaxyPrediction of HLA binding for verified candidates
Associated Tutorial
This workflows is part of the tutorial Neoantigen 5a: Predicting HLA Binding, available in the GTN
Features
- Includes a Galaxy Workflow Report
Thanks to...
Workflow Author(s): galaxyp
Tutorial Author(s): Subina Mehta, Katherine Do, James Johnson
Tutorial Contributor(s): Pratik Jagtap, Timothy J. Griffin, Subina Mehta, Saskia Hiltemann, Katherine Do
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| R1.fastq | #main/R1.fastq | Paired RNAseq forward reads. |
|
| R2.fastq | #main/R2.fastq | Paired RNAseq reverse reads. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 2 | Optitype | HLA genotyping output toolshed.g2.bx.psu.edu/repos/iuc/optitype/optitype/1.3.5+galaxy0 |
| 3 | seq2HLA | HLA genotyping output toolshed.g2.bx.psu.edu/repos/iuc/seq2hla/seq2hla/2.3+galaxy0 |
| 4 | Reformated-Optitype-Data | reformatting the data to make it easy to interpret toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1 |
| 5 | IEDB_alleles | extract IEDB alleles toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| IEDB-Optitype-seq2HLA-alleles | #main/IEDB-Optitype-seq2HLA-alleles | n/a |
|
| IEDB_Optitype_alleles | #main/IEDB_Optitype_alleles | n/a |
|
| IEDB_seq2HLA_alleles | #main/IEDB_seq2HLA_alleles | n/a |
|
| OptiType_on_input_datasets_coverage_plot | #main/OptiType_on_input_datasets_coverage_plot | n/a |
|
| OptiType_on_input_datasets_result | #main/OptiType_on_input_datasets_result | n/a |
|
| Reformated-Optitype-Data | #main/Reformated-Optitype-Data | n/a |
|
| seq2HLA_genotype_4digits | #main/seq2HLA_genotype_4digits | n/a |
|
Version History
master
Creators and Submitter
Views: 831 Downloads: 132 Runs: 0
Created: 7th Jul 2025 at 14:16
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