QorTs.txt

# Step 1: Initial Data Processing
mkdir -p outputData/qortsQcData/SAMP1_RG1/

java -Xmx1G -jar softwareRelease/QoRTs.jar QC --stranded --chromSizes inputData/annoFiles/chrom.sizes inputData/bamFiles/SAMP1_RG1.bam inputData/annoFiles/anno.gtf.gz outputData/qortsQcData/SAMP1_RG1/

# Step 2: Generating Counts and QC plots
res <- read.qc.results.data("outputData/qortsData/", decoder.files = "inputData/annoFiles/decoder.byUID.txt", calc.DESeq2 = TRUE, calc.edgeR = TRUE);

# Step 4: Merge Technical Replicates
java -jar softwareRelease/QoRTs.jar mergeAllCounts outputData/qortsData/ inputData/annoFiles/decoder.byUID.txt outputData/countTables/

# Step 6: Perform Differential Splicing Analyses
java -Xmx1G -jar softwareRelease/QoRTs.jar makeFlatGff --stranded inputData/annoFiles/anno.gtf.gz outputData/forJunctionSeq.gff.gz

# Add Novel Junctions
java -Xmx1G -jar softwareRelease/QoRTs.jar mergeNovelSplices --minCount 6 --stranded outputData/countTables/ outputData/sizeFactors.GEO.txt inputData/annoFiles/anno.gtf.gz outputData/countTables/

# Perform Analysis with JunctionSeq
source("http://hartleys.github.io/JunctionSeq/install/JS.install.R")
JS.install()

# Step 7: Generating Browser Tracks
java -Xmx1G -jar softwareRelease/QoRTs.jar bamToWiggle --stranded --windowSize 100 --negativeReverseStrand --includeTrackDefLine --rgbColor 0,0,0 inputData/bamFiles/SAMP1_RG1.bam SAMP1_RG1 inputData/annoFiles/chrom.sizes outputData/qortsData/SAMP1_RG1/QC.wiggle