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configure
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configure
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## ***************************************************
#
# this is the configuration file for the pipeline icSHAPE
# options specified when running the wrapper shape_seq.pl will override settings here
# the purpose of this file is to set some more stable parameters and
# some complex parameters that would be too clumsy to set in command line options
# the format is like: key value
#
## -----
# Copyright qczhang@stanford.edu, Sept. 20, 2013
#
## ***************************************************
#
FASTQCODING phred33
### fastq file quality coding used in trimming and alignment
#
COLLAPSEBIN $ICSHAPE/scripts/readCollapse.pl
### read collapse script to remove PCR duplcates
COLLAPSEFASTA collapse.fa
### output fastq file from read collapse script
#
JAVABIN /usr/java/latest/bin/java
### location of system java
TRIMMER $ICSHAPE/scripts/trimming.pl
### trimming script to remove 3' adaptor and 5' barcodes
TRIMLOG trimming.log
### log file of trimming running
ADAPTER $ICSHAPE/data/TruSeq2-PE.fa
### location of adaptor sequence used in trimming programs
LEADINGTRIM 13
### length of 5' barcode to be trimmed off
TAILINGTRIM 0
### length of 3' sequence to be trimmed off
TRIMMINLEN 25
### minimum length of reads to keep
#
ALIGNER /srv/gs1/software/bowtie/2.0.5/bowtie2
### location of reads alignment tool
#MAPPINGREF $BOWTIELIB/mouse/ensembl.transcriptome
MAPPINGREF $ICSHAPE/data/bowtieLib/nanog
### location of mapping library
MAPPINGOPTIONS "--non-deterministic --time"
### mapping options to be passed to aligner
#
ESTIMATERPKM $ICSHAPE/scripts/estimateRPKM.pl
### script to estimate transcript abundance
MINLOAD 5
### load cutoff to keep transcripts after abundance estimation
CALCRT $ICSHAPE/scripts/calcRT.pl
### script to calculate raw RT scores at each position of nucleotide
#
CORRELATEBIN $ICSHAPE/scripts/correlationRT.pl
### script to calculate transcript correlations in each replicate
COMBINEBIN $ICSHAPE/scripts/combineRTreplicates.pl
### script to combine replicates
#
NORMALIZEBIN $ICSHAPE/scripts/normalizeRTfile.pl
### script to normalize RT scores
HEADTOSKIP 32
### length of leading postions in each transcript to skip in normalization
TAILTOSKIP 32
### length of tailing postions in each transcript to skip in normalization
METHOD mean:vigintile2
### string to define normalization method: "mean" means to calculate the mean value, and "vigintile2" means to select the second highest vigintile
#
CALCENRICHBIN $ICSHAPE/scripts/calcEnrich.pl
### script to calculate enrichment scores from target and background RT profiles
WINSOR factor5:scaling1
### string to define winsorization method
DIVFACTOR 10
SUBFACTOR 0.25
### alpha and beta parameter defined in the icSHAPE paper, used to calculate icSHAPE reactivity scores
#
FILTERENRICH $ICSHAPE/scripts/filterEnrich.pl
### script to select enrichment scores from raw scores by some cutoffs
### the following are parameters to define cutoffs for selecting valid enrichment scores.
INPUTCOVERAGE 200
### the background sequencing cutoff
TARGETHIT 2
### the target hit-level
HEADTOSKIP 5
### number of heading nuclueotides to be skipped in the selection
TAILTOSKIP 30
### number of tailing nuclueotides to be skipped in the selection
#
SHAPE2BEDGRAPGH $ICSHAPE/scripts/shape2Bedgraph.pl
### script to conver transcript shape score to genome bedgraph file
BEDGRAPH2BIGWIG /srv/gs1/software/ucsc_tools/2.7.2/bin/x86_64/bedGraphToBigWig
### tool to convert bedgraph format to big wig format
GENOMESIZE /home/qczhang/database/ensembl/current/mouse/dna/genome.sm.chr.size
### genome size file that contains the informaiton of each sequence(usally chromosomes or scaffolds) length. To be used to convert bedgraph to bigwig.
#
##----------------------------------------------------
#