GigaScience-RNAseq-Optitype-seq2HLA-to-IEDB-alleles
1.0

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Workflow Type: Galaxy

Prediction of HLA binding for verified candidates

Associated Tutorial

This workflows is part of the tutorial Neoantigen 6: Predicting HLA Binding, available in the GTN

Features

Thanks to...

Workflow Author(s): galaxyp

Tutorial Author(s): Subina Mehta, Katherine Do, James Johnson

Tutorial Contributor(s): Pratik Jagtap, Timothy J. Griffin

gtn star logo followed by the word workflows

SEEK ID: https://dev.workflowhub.eu/workflows/1381?version=1

Inputs

ID Name Description Type
R1.fastq #main/R1.fastq Paired RNAseq forward reads.
  • File
R2.fastq #main/R2.fastq Paired RNAseq reverse reads.
  • File

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
  • File
IEDB_Optitype_alleles #main/IEDB_Optitype_alleles n/a
  • File
IEDB_seq2HLA_alleles #main/IEDB_seq2HLA_alleles n/a
  • File
OptiType_on_input_datasets_coverage_plot #main/OptiType_on_input_datasets_coverage_plot n/a
  • File
OptiType_on_input_datasets_result #main/OptiType_on_input_datasets_result n/a
  • File
Reformated-Optitype-Data #main/Reformated-Optitype-Data n/a
  • File
seq2HLA_genotype_4digits #main/seq2HLA_genotype_4digits n/a
  • File

Version History

1.0 (earliest) Created 20th Jan 2025 at 13:07 by Helena Rasche

Added/updated 4 files


Open master ff54ab2
help Creators and Submitter
Creators
Not specified
Submitter
Tools
OptiType
Seq2HLA
License
No license - no permission to use unless the owner grants a licence
Activity

Views: 21   Downloads: 7

Created: 20th Jan 2025 at 13:07

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Total size: 117 KB
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