GigaScience_Peptide_Annotation_demonstration_STS26T_neoantigen_candidates

Annotating the novel peptides

Associated Tutorial

This workflows is part of the tutorial Neoantigen 5: Variant Annotation, 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

Inputs

ID	Name	Description	Type
Annotated-GffCompared-GTFtoBED	#main/Annotated-GffCompared-GTFtoBED	Annotated GffCompared GTF to BED	File
Fragpipe-Peptide-Report	#main/Fragpipe-Peptide-Report	Peptide report from Fragpipe workflow	File
Homo_sapiens.GRCh38_canon.106.gtf	#main/Homo_sapiens.GRCh38_canon.106.gtf	Homo_sapiens.GRCh38_canon.106.gtf	File
Novel_Peptides	#main/Novel_Peptides	Candidate Neoantigens from Fragpipe Workflow	File

Steps

ID	Name	Description
4	Peptide_to_Protein_Annotation	Extracting the information from Fragpipe for the Novel peptides toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
5	FASTA-IEDB	FASTA file for IEDB toolshed.g2.bx.psu.edu/repos/devteam/tabular_to_fasta/tab2fasta/1.1.1
6	Converting_pipes_to_columns	converting pipes to columns Convert characters1
7	Modifying-string-name	Modifying-string-name toolshed.g2.bx.psu.edu/repos/galaxyp/regex_find_replace/regexColumn1/1.0.3
8	Converting_colons_to_columns	converting colons to columns Convert characters1
9	Extracting-info-from-GFFtobed	Extracting-info-from-GFFtobed toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
10	Table-processing-3	multiplying start and stop of the peptide location with 3 to calculate genomic coordinates toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
11	Peptide-location-generation	calculation genomic coordinates looking at peptide location toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
12	BED-File-for-PepPointer	Extracting bed file for Peppointer toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2
13	PepPointer	PepPointer to add annotation to the peptides at Genomic level toolshed.g2.bx.psu.edu/repos/galaxyp/pep_pointer/pep_pointer/0.1.3+galaxy1
14	Summary-Neoantigen	Summary file for Neoantigen toolshed.g2.bx.psu.edu/repos/iuc/query_tabular/query_tabular/3.3.2

Outputs

ID	Name	Description	Type
BED-File-for-PepPointer	#main/BED-File-for-PepPointer	n/a	File
Extracting-info-from-GFFtobed	#main/Extracting-info-from-GFFtobed	n/a	File
FASTA-IEDB	#main/FASTA-IEDB	n/a	File
Modified-string-name	#main/Modified-string-name	n/a	File
Neoantigen_summary	#main/Neoantigen_summary	n/a	File
PepPointer-Annotated-Peptides	#main/PepPointer-Annotated-Peptides	n/a	File
Peptide-location-generation	#main/Peptide-location-generation	n/a	File
Peptide_to_Protein_Annotation	#main/Peptide_to_Protein_Annotation	n/a	File
Table-processing-1	#main/Table-processing-1	n/a	File
Table-processing-2	#main/Table-processing-2	n/a	File
Table-processing-3	#main/Table-processing-3	n/a	File

Version History

Added/updated 4 files

Open master fae1431

Added/updated 4 files

Frozen 1.0 c919910