script/debug-STAR.R

In uzh/ezRun: An R meta-package for the analysis of Next Generation Sequencing Data

setwd("/srv/GT/analysis/gtan/p2438-STAR/2-pass")
Sys.setenv("PATH"=paste("/usr/local/ngseq/packages/Dev/Python2/2.7.13/bin", Sys.getenv("PATH"), sep=":"))
library(ezRun)
param = list()
param[['cores']] = '8'
param[['ram']] = '40'
param[['scratch']] = '100'
param[['node']] = ''
param[['process_mode']] = 'SAMPLE'
param[['refBuild']] = 'Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_89-2017-05-31'
param[['paired']] = 'false'
param[['strandMode']] = 'antisense'
param[['refFeatureFile']] = 'genes.gtf'
param[['cmdOptions']] = '--outFilterType BySJout --outFilterMatchNmin 30 --outFilterMismatchNmax 10 --outFilterMismatchNoverLmax 0.05 --alignSJDBoverhangMin 1 --alignSJoverhangMin 8 --alignIntronMax 1000000 --alignMatesGapMax 1000000 --outFilterMultimapNmax 50 --chimSegmentMin 15 --chimJunctionOverhangMin 15 --chimScoreMin 15 --chimScoreSeparation 10 --outSAMstrandField intronMotif'
param[['getChimericJunctions']] = 'false'
param[['trimAdapter']] = 'true'
param[['trimLeft']] = '5'
param[['trimRight']] = '0'
param[['minTailQuality']] = '10'
param[['minAvgQuality']] = '10'
param[['minReadLength']] = '20'
param[['specialOptions']] = ''
param[['mail']] = 'ge.tan@fgcz.ethz.ch'
param[['dataRoot']] = '/srv/gstore/projects'
param[['resultDir']] = 'p2438/STAR_18564_2017-06-12--13-46-30'
param[['twopassMode']] = "true" #false
output = list()
output[['Name']] = '53KW_d3_A'
output[['BAM [File]']] = 'p2438/STAR_18564_2017-06-12--13-46-30/53KW_d3_A.bam'
output[['BAI [File]']] = 'p2438/STAR_18564_2017-06-12--13-46-30/53KW_d3_A.bam.bai'
output[['IGV Starter [Link]']] = 'p2438/STAR_18564_2017-06-12--13-46-30/53KW_d3_A-igv.jnlp'
output[['Species']] = 'Homo sapiens (human)'
output[['refBuild']] = 'Homo_sapiens/Ensembl/GRCh38.p10/Annotation/Release_89-2017-05-31'
output[['paired']] = 'false'
output[['refFeatureFile']] = 'genes.gtf'
output[['strandMode']] = 'antisense'
output[['Read Count']] = '39534111'
output[['IGV Starter [File]']] = 'p2438/STAR_18564_2017-06-12--13-46-30/53KW_d3_A-igv.jnlp'
output[['IGV Session [File]']] = 'p2438/STAR_18564_2017-06-12--13-46-30/53KW_d3_A-igv.xml'
output[['PreprocessingLog [File]']] = 'p2438/STAR_18564_2017-06-12--13-46-30/53KW_d3_A_preprocessing.log'
output[['STARLog [File]']] = 'p2438/STAR_18564_2017-06-12--13-46-30/53KW_d3_A_STAR.log'
output[['Condition [Factor]']] = 'asthmatic'
output[['Extract Id [B-Fabric]']] = 'bfe_53715'
input = list()
input[['Name']] = '53KW_d3_A'
input[['Condition']] = 'asthmatic'
input[['Read1']] = 'p2438/HiSeq4000_20170601_RUN346_copy_o3365/20170601.B-53KW_d3_R1.fastq.gz'
input[['Species']] = 'Homo sapiens (human)'
input[['FragmentSize']] = '0'
input[['SampleConc']] = '9.1'
input[['Tube']] = 'p2438_3365/24'
input[['Extract Id']] = 'bfe_53715'
input[['Index']] = 'GAATTCGT-CAGGACGT'
input[['PlatePosition']] = '1_G6'
input[['LibConc_100_800bp']] = '1.75'
input[['LibConc_qPCR']] = '0'
input[['Adapter1']] = 'GATCGGAAGAGCACACGTCTGAACTCCAGTCAC'
input[['strandMode']] = 'antisense'
input[['LibraryPrepKit']] = 'TruSeq RNA stranded'
input[['EnrichmentMethod']] = 'PolyA, TruSeq RNA Kit'
input[['InputAmount']] = '100'
input[['Read Count']] = '39534111'
input[['Time']] = 'd3'
input[['Age']] = '22'
input[['Gender']] = 'F'
EzAppSTAR$new()$run(input=input, output=output, param=param)

## debug 
input = EzDataset$new(meta=input, dataRoot=param$dataRoot)
output = EzDataset$new(meta=output, dataRoot=param$dataRoot)
param = ezParam(param, appDefaults=appDefaults)