Introduction

Rapid Prioritization of Tumor Antigens from Immunopeptides!

Arguments

Long	Short	Value	Description	Default	Mandatory
input	i	string (.tsv)	input file path	NA	Y
bam	b	string (.bam)	bam file path	NA	Y
output	o	string	output file path	NA	Y
mode	m	scan, target	mode of match	target	N
sequence	s	peptide, nucleotide	sequence type	peptide	N
count	c	primary, all	type of countable reads	primary	N
equal	e	NA	I is equivalent to L (only available for scan mode)	NA	N
thread	@	integer	the number of threads	4	N

Quick examples

java -Xmx2G -jar bamscan.jar -i test_scan.tsv -b test.bam -o test_scan.scan -m scan -s peptide -e
java -Xmx2G -jar bamscan.jar -i test_target.tsv -b test.bam -o test_target.target -m target -s peptide

Input

A tab-separated value (TSV) format is allowed. This file should include a header.

Scan mode

Sequence	Any column 1	Any column 2	...	Any column N
AAIPPIVTK	Any content 1	Any content 2	...	Any content N
FPWQEHEA	Any content 1	Any content 2	...	Any content N

Target mode

Sequence	Location	Strand	...	Any column N
AAIPPIVTK	Any content 1	Any content 2	...	Any content N
FPWQEHEA	Any content 1	Any content 2	...	Any content N

Bam

Bam file must be sorted by a genomic coordinate and indexed (.bai must exist in the same folder).

Mode

• Scan mode: It counts all reads matching the given sequences by traversing all reads and annotates their genomic information
• Target mode: It counts all reads matching the given 3-tuple <Sequence, Location, Strand>. Target mode requires .bai in advance.

Equal

The option is not necessary when you know exact sequences. If you identified peptide sequences from MS/MS spectra, we recommend to set this option. This is because there are chances that the sequences are ambiguous about I/L decision in MS/MS sequencing.