Commit 2e7e306a authored by psimion's avatar psimion
Browse files

default tool is now kallisto

parent 8795a3aa
TOOL=R # B for Bowtie, K for kallisto or S for Salmon
TOOL=K # B for Bowtie, K for kallisto or S for Salmon
INDIR=$(pwd) # name of the input directory
FOLD=2 # how many fold enrichment of correct source over others is required to keep
MINCOV=0.2 # min coverage of contig by "own's" read to
......
TOOL=K # B for Bowtie, K for kallisto or S for Salmon
INDIR=$(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
CLEANING=no # cleaning reads from fastq files if they correspond to cross contaminant transcripts
......@@ -87,7 +87,7 @@ for ref in "${orders[@]}"; do
done
# cleaning up files
mv $out/*.index $out/utility_files_CroCo
mv $out/*.index $out/*.reads_to_discard $out/utility_files_CroCo
rm -f $out/*.gunziped
rm -f $out/*.contigstotrim
rm -f $out/*.badcontigs
......
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