# # ABACUS parameter file # Generated on: 2017Feb07_1919 # # Name to give the database dbName=ABACUSDB # Name of protXML file corresponding to merged/combined results combinedFile=/home/srlab/Documents/rhonda/./interact-COMBINED.prot.xml # The directory that contains the pepXML and protXML files srcDir=/home/srlab/Documents/rhonda # The name of the file where results will be saved to outputFile=/home/srlab/Documents/rhonda/ABACUS_output.tsv # The minimum PeptideProphet score the best peptide match of a protein must have maxIniProbTH=0.99 # The minimum PeptideProphet score a peptide must have in order to be even considered by Abacus iniProbTH=0.50 # E.P.I: Experimental Peptide-probability Inclusion threshold # If a protein does not contain at least one peptide exceeding this PeptideProphet score, none of the # peptide evidence for this protein will be considered. This is applied on an experiment by experiment case. epiTH=0 # The minimum ProteinProphet score a protein group must have in the COMBINED file minCombinedFilePw=0.90 # The path the the FASTA formatted file used for the original protein search # Relative paths are allowed fasta=/home/srlab/Documents/rhonda/contigs.fasta.transdecoder.pep # If true, Abacus will write ALL protein IDs belonging to a group in the COMBINED file # Protein IDs starting with ':::' are additional identifiers from the same protein group in # the COMBINED file. The representative protein for the group does not start with ':::' verboseResults=false # The keep the HyperSQL database files that are created after the program is done keepDB=false # Should the peptide weights be recalculated in the individual experiment XML files. # Useful for peptides that are highly degenerate within a single protein groups recalcPepWts=false # Spectral count data will be reported in NSAF format. # NSAF = _N_ormalized _S_pectral _A_bundance _F_actor # For a detailed explanation of this method refer to this pubmed link: # http://www.ncbi.nlm.nih.gov/pubmed/20166708 # Abacus reports NSAF values multiplied by a scaling factor. This is done to # control for numeric underflow (ie: really small numbers). The scaling factor # that is used is called the NSAF_FACTOR and is reported during runtime in # case you would like to rescale your data. asNSAF=false # If you are using decoy proteins in your searches, specify the first few # characters of the label indicating decoy proteins here decoyTag=rev_ # Output format that will be produced by this parameter file output=default