PepQueryMHC

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• About
• Usage
  • Quick start
  • Parameters
  • Scan mode
  • Target mode
  • FASTQ mode
  • Annotate mode
• Figures for the reviewers
• License

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About

The accurate prioritization of tumor antigens, including aberrant translational products, is critical for the development of personalized cancer immunotherapies. PepQueryMHC estimates a comprehensive repertoire of local RNA expression of tumor antigens within minutes per sample.

Usage

PepQueryMHC provides three main functions such as 1) scan mode, 2) target mode 3) FASTQ mode and 4) annotate mode.
When you use FASTQ mode, please make sure that FASTQ files do not contain artifical sequences such as adaptors, barcodes and so on.

Quick start

Scan mode

java -Xmx2G -jar PepQueryMHC.jar \
--mode scan \
--input peptides.tsv \
--bam sample.sorted.bam \
--output sample \
--thread 16

Target mode

java -Xmx2G -jar PepQueryMHC.jar \
--mode target \
--input peptides_locations_strands.tsv \
--bam sample.sorted.bam \
--output sample \
--thread 16

FASTQ mode (for single-end)

java -Xmx2G -jar PepQueryMHC.jar \
--mode fastq \
--input peptides.tsv \
--0 sample.trimmed.fastq.gz \
--output sample \
--strand f \
--thread 16

FASTQ mode (for paired-end)

java -Xmx2G -jar PepQueryMHC.jar \
--mode fastq \
--input peptides.tsv \
--1 sample.trimmed.fastq.1.gz \
--2 sample.trimmed.fastq.2.gz \
--output sample \
--strand rf \
--thread 16

Annotate mode

java -Xmx2G -jar PepQueryMHC.jar \
--mode annotate \
--input locations_strands.tsv \
--gtf reference_annotation.gtf \
--output sample

Parameters

Y+: mandatory, Y: optional, N: none

Option	Description	Type	Default	Scan mode	Target mode	FASTQ mode	Annotate mode
m/mode	mode to use	scan|target|fastq|annotate		Y+	Y+	Y+	Y+
i/input	input file path	string		Y+	Y+	Y+	Y+
o/output	output base name path	string		Y+	Y+	Y+	Y+
b/bam	sorted bam/sam file path	bam|sam		Y+	Y+	N	N
0/fastq_single	fastq file path	fastq|fastq.gz		N	N	Y+	N
1/fastq_paired_1	fastq file path	fastq|fastq.gz		N	N	Y+	N
2/fastq_paried_2	fastq file path	fastq|fastq.gz		N	N	Y+	N
g/gtf	gtf file path	string		N	N	N	Y+
@/thread	the number of threads	int	4	Y	Y	Y	N
c/count	tpye of reads being processed	primary|all	primary	Y	Y	N	N
l/lib_size	tsv file including library size information	string		Y	Y	Y	N
w/white_list	cell brcode list (tsv), only available in single-cell RNA-seq	string		Y	Y	Y	N
p/prob	ignore region of interests with error > p	[0,1]	0.05	Y	Y	Y	N
e/equal	specify isoleucine = leucine	none		Y	Y	Y	N
u/union	specify the unit of the peptide read count	sum|max	sum	Y	Y	N	N
s/strand	specify strandedness. non: non-stranded, fr: fr-second strand, rf: fr-first strand, f: forward strand for single-end, r: reverse strand for single-end, auto: auto-detection. Auto-detection is only available if there is XS tag in a given bam file	non|fr|rf|f|r|auto	auto	Y	Y	Y+	N
s/stretch	output single line per annotation	none		N	N	N	Y
v/verbose	print every messages being processed	none		Y	Y	Y	Y

Scan mode

Input format

Sequence	User-defined column 1	...	User-defined column N
AACTKLAKKM	any value	...	any value

Target mode

Input format

Sequence	Location	Strand	User-defined column 1	...	User-defined column N
AACTKLAKKM	chr1:1-30	+	any value	...	any value
TKMQEPPALY	chr1:31-50|chr1:81-90	-	any value	...	any value
KEKRKAPPR	.	.	any value	...	any value

FASTQ mode

Input format

Sequence	User-defined column 1	...	User-defined column N
AACTKLAKKM	any value	...	any value

• input format is exactly the same as what used in scan mode.

Annotate mode

Input format

Location	Strand	User-defined column 1	...	User-defined column N
chr1:1-30	+	any value	...	any value
chr1:31-50|chr1:81-90	-	any value	...	any value
chr1:21-40|chr1:87-90	.	any value	...	any value

Figures for the reviewers

Figures in the paper can be generated using: 1) R code in figR folder, 2) Supplementary Tables 1,2,3, and 5, and 3) the meta dataset available at https://doi.org/10.5281/zenodo.14984543.

License

All code is available as under the Attribution-NonCommercial (CC BY-NC) 4.0 license.