def_values.sh~ 1.2 KB
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TOOL=R   # B for Bowtie, K for kallisto or S for Salmon
INDIR=$(pwd)   # name of the input directory
FOLD=2   # how many fold enrichment of correct source over others is required to keep
MINCOV=0.2   # min coverage of contig by "own's" read to
PROCESSORS=1   # number of threads for running the tool
OUTPUTPREFIX=""   # prefix of output directory that will be created
OUTPUTLEVEL=2   # "verbosity" level for fasta outputs
GRAPH=no   # wether to produce a graphical output of the crosscontamination network
ADDOPT=""   # string that will be added to the mapper command line
TRIM5=0   # number of bases to trim from read's 5'
TRIM3=0   # number of bases to trim from read's 3'
FRAGLENGTH=none   # average fragment length
FRAGSD=none   # standard deviation of fragment length
SUSPID=95   # blast minimum id% for being a potential suspect of cross contamination
SUSPLEN=40   # blast minimum id% for being a potential suspect of cross contamination
OVEREXP=300   # expression level (TPM) above which a transcript might be considered "overexpressed"
RECAT=no   # previous CroCo output directory to be used to re-categorize transcripts
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CLEANING=no	# cleaning reads from fastq files if they correspond to cross contaminant transcripts