Module name: summary-crapome

Generates a CRAPome matrix from SAINT input files

parameters	definition	default
baitFiles	bait.dat: files with bait sample IDs, bait name and control status (C: control, T: non-control)
crapomeID	text file with two columns containing sample name with ID as ID_name and CRAPome CC number
interactionFiles	inter.dat: files with bait ID and name, prey accession and spectral count
outFile	output matrix	crapome-matrix.txt
preyFiles	prey.dat: files with prey accession, sequence length and gene name

Multiple SAINT tasks can be merged by listing multiple bait.dat, inter.dat and prey.dat files separated by a semicolon. Each of these should be listed in a consistent order:

-baitFiles="bait-task1.dat;bait-task2.dat" -interactionFiles="inter-task1.dat;inter-task2.dat" -preyFiles="prey-task1.dat;prey-task2.dat"

Example file formats

baitFile (bait.dat)

header: projectID_sampleID | bait name | control status

128_468	ACTB	T
128_492	ACTB	T
128_590	ATP2A1	T
128_546	ATP2A1	T
128_737	737_BirAFLAG	C
128_825	825_BirAFLAG	C

crapomeID

filename	cc
9522_BirAFLAG_April2017_Go_RIPA_07012018.raw	CC1100
9221_BirAFLAG_HighDen_Go_KA_RIPA_10112017_BR1.raw	CC1101
7909_BirAFLAG_April2017_Go_RIPA_06042017_TR1.raw	CC1102
7024_BirAFLAG_May2016_test_Go_RIPA_31102016_TR1	CC1103
7015_BirAFLAG_May2016_Go_RIPA_31102016_TR1.raw	CC1104

interactionFile (inter.dat)

header: projectID_sampleID | bait name | prey accession | spectral count | unique peptides |

128_468	ACTB	BirA_R118G_H0QFJ5	1410	23
128_468	ACTB	NP_000029.2	4	3
128_468	ACTB	NP_000108.1	2	2
128_468	ACTB	NP_000280.1	3	2
128_468	ACTB	NP_000402.3	11	10
128_468	ACTB	NP_000652.2	7	5

preyFile (prey.dat)

header: accession | prey sequence length | prey name |

BirA_R118G_H0QFJ5	321	BirA_R118G_H0QFJ5
NP_000029.2	2843	APC
NP_000108.1	254	EMD
NP_000280.1	780	PFKM
NP_000402.3	726	HLCS
NP_000652.2	192	RPL9
NP_000911.2	1178	PC

Output

• txt matrix file formatted for CRAPome with prey summaries across control samples