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p3.config
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p3.config
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# This is configuration file for P3. http://github.com/kristiyanto/p3
[SOURCE]
# REPO = LOCAL/FTP/PRIDE
REPO = LOCAL
# If REPO = FTP, at least FTP_1 is required.
# e.g:
# FTP_1 = ftp://massive.ucsd.edu/MSV000079527/sequence/
# FTP_2 = ftp://massive.ucsd.edu/MSV000079527/peak/mgf/
FTP_1 = ftp://massive.ucsd.edu/MSV000079527/sequence/
FTP_2 = ftp://massive.ucsd.edu/MSV000079527/peak/mgf/
# if REPO = PRIDEID, PRIDEID must be defined
# e.g
# PRIDEID = PXD000001
PRIDEID =
[MSGF]
# RUN_MSGF = YES / NO ; if NO, MSGF identification will be skipped.
# e.g:
# RUN_MSGF = YES
RUN_MSGF = YES
# MSGF_OPTIONS: OPTIONAL. Additional options for identification other than -s -d and -o
# Check https://omics.pnl.gov/software/ms-gf for more detail
# e.g
# -t = 10ppm
# -m = 0
# -inst = 1
# -e = 1
# -ti = -1,2
# -ntt = 2
# -tda = 1
# -minLength = 6
# -maxLength = 50
# -minCharge = 2
# -maxCharge = 5
# -n = 1
# -thread = 7
# -mod = MSGFDB_Mods.txt
# -minNumPeaks = 5
# -addFeatures = 1
[QUANTIFICATION]
# METHOD = SPECTRUM_COUNT / ITRAQ4 / NONE
# If "NONE", quantification will not be run.
# e.g
# METHOD = SPECTRUM_COUNT
METHOD = SPECTRUM_COUNT
[SPECTRUM_COUNT]
# This section is ignored if QUANTIFICATION METHOD is not SPECTRUM_COUNT
# If left blank filtering will not be performed
SPEC_EVALUE_TRESHOLD = 1e-10
# COMBINE_BY will perform feature folding with the specified function. If "SKIP" is given, this task will not be performed.
# COMBINE_BY: SKIP / mean / median / weighted.mean / sum / medpolish
COMBINE_BY = mean
[ITRAQ4]
# This section is ignored if QUANTIFICATION METHOD is not ITRAQ4
# If left blank filtering will not be performed
SPEC_EVALUE_TRESHOLD = 1e-10
pNA = 4
# QUANTIFICATION_METHOD: / trapezoidation / max / sum / SI / SIgi / SIn / SAF / NSAF
# *CASE SENSITIVE*
QUANTIFICATION_METHOD = max
# COMBINE_BY will perform feature folding with the specified function. If "SKIP" is given, this task will not be performed.
# COMBINE_BY: SKIP / mean / median / weighted.mean / sum / medpolish
COMBINE_BY = mean
# OPTIONAL
# MAXWAIT = 10800 # Optional. How long the container will wait for other containers
# to finish when multiple containers are running concurrently.