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pipelineConfiguration.sample.yaml
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pipelineConfiguration.sample.yaml
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ReferenceData:
genomeRootFolder: /data/genomes
targetscanFolder: /data/targetscan
mirbaseFolder: /data/mirbase
BowtieMapSingleReads:
mappingSoftware: /usr/local/bin/bowtie
host: hsa
alignmentMode: v
noOfMismatches: 2
ParseSAMForMiRNAs:
baselinePercent: 5
host: hsa
analyzeIsomirs: true
mirbaseVersion: 20
bleed: 2
DEwithEdgeR:
host: hsa
pValue: 2
mirbaseVersion: 20
UnzipInputFiles:
noOfThreads: 4
unzipSoftware: /usr/local/pigz
CollapseReads:
fastq2fastaLocation: /usr/local/bin/fastq_to_fasta
fastxCollapserLocation: /usr/local/bin/fastx_collapser
SingleReadAdapterTrim:
adapterSoftware: /Users/simonray/software/trimmomatic/Trimmomatic-0.33/trimmomatic-0.33.jar
adapterFile: /Users/simonray/NetBeansProjects/SmallRNAPipeline/test/TruSeqE-SE.fa
minAvgReadQual: 30
minAlignScore: 7
noOfThreads: 4
noOfMismatches: 2
BSMapReads:
reportUnmappedReads: false
mappingStrand: 0
startAtThisRead: 1
threeNucleoideMapping: false
reportRepeatsValue: 1
skipSAMHeader: false
endtAtThisRead: -1
gapSize: 0
host: hsa
transitionMap: TC
minInsertSize: 28
lowQualityFilterValue: 5
mapFirstNucleotides: 0
trimAdapterSequence: true
includeRefSeq: false
maxInsertSize: 500
noOfMismatches: 0.08
randomSeed: 0
adapterSequence:
- GATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATCTCGTATGCCGTCTTCTGCTTG
- AATGATACGGCGACCACCGAGATCTACACTCTTTCCCTACACGACGCTCTTCCGATCT
kmerCutoffRatio: 1.0E-6
genomeIndexInterval: 4
pathToBSmap: /usr/local/bin/bsmap
digestionSite: C-CGG
messageLevel: 1
'seedSize:': 16
qualityThresholdTrimValue: 0
noOfThreads: 4
AnalyzeStartPositions:
baselinePercent: 5
minCounts: 1000
featureSeparation: 10
host: hsa
longestFeature: 2
mirbaseVersion: 20
bleed: 2
shortestFeature: 2
CleanUp:
noOfThreads: 4
unzipSoftware: /usr/local/pigz
fileTypes:
- fastq
- fasta
- sam