GigaScience_PepQuery2_demonstration_STS26T_neoantigen_candidates_workflow
1.0

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Workflow Type: Galaxy

Validate the NeoAntigen Candidates from FragPipe discovery through the PepQuery Novel search

Associated Tutorial

This workflows is part of the tutorial Neoantigen 4: PepQuery2 Verification, available in the GTN

Workflow Author(s): GalaxyP

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

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

SEEK ID: https://dev.workflowhub.eu/workflows/1387?version=1

ID	Name	Description	Type
Candidate_Neoantigens	#main/Candidate_Neoantigens	Candidate Neoantigens from Fragpipe Workflow	File
HUMAN_Uniprot_and_CRAP.fasta	#main/HUMAN_Uniprot_and_CRAP.fasta	Known human and contaminant protein fasta database	File
Human-TAX-ID	#main/Human-TAX-ID	this is for blastP taxid restrictions- homo sapiens-9606	File
Input Raw-files	#main/Input Raw-files	RAW File	File

ID	Name	Description
4	Converting_RAW_to_MGF	Converting Raw to MGF toolshed.g2.bx.psu.edu/repos/galaxyp/msconvert/msconvert/3.0.20287.2
5	PepQuery2	PepQuery against HUMAN and contaminants to know filter peptides that doesn't match to anything in the known Uniprot database toolshed.g2.bx.psu.edu/repos/galaxyp/pepquery2/pepquery2/2.0.2+galaxy2
6	PepQuery_Validated_Peptides	Extract Peptides with the confident column as "Yes" toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
7	Getting-blast-ready	toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1
8	BLAST-Protein	BLAST-Protein against swissprot, ref seq and NCBI NR and filtering for HUMAN only results toolshed.g2.bx.psu.edu/repos/devteam/ncbi_blast_plus/ncbi_blastp_wrapper/2.14.1+galaxy2
9	Novel_Peptides_from_PepQuery	Extracting Novel peptides after BlastP toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2

ID	Name	Description	Type
BLAST-P-READY-Peptides	#main/BLAST-P-READY-Peptides	n/a	File
BlastP-output	#main/BlastP-output	n/a	File
Novel_Peptides_from_PepQuery	#main/Novel_Peptides_from_PepQuery	n/a	File
PepQuery_Validated_Peptides	#main/PepQuery_Validated_Peptides	n/a	File
PepQuery_psm_rank_txt	#main/PepQuery_psm_rank_txt	n/a	File