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exampleRiboPipeConigFile.conf
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exampleRiboPipeConigFile.conf
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export PATH_TO_rRNA_INDEX=/projects/bowtie-1.1.1-indices/Saccharomyces_cerevisiae/index_rRNA/
export PATH_TO_GENOME_INDEX=/projects/STAR_indices/star-2.5-Scerevisiae/STAR_2.5_overHang30/
export PATH_TO_REFERENCE_TRANSCRIPTOME_FILE=/projects/transcriptomes/Saccharomyces_cerevisiae/ensemble86_RM64_1/Saccharomyces_cerevisiae.R64-1-1.cdna.all.faSaccharomyces_cerevisiae.R64-1-1.cdna.all.fa
export PATH_TO_ANNOTATION_FILE=/projects/annotations/GTF/Ensembl_81/Saccharomyces_cerevisiae.R64-1-1.81.gtf
export PATH_TO_REFERENCE_GENOME_FILE=/projects/genomes/Ensembl_85/saccharomyces_cerevisiae/Saccharomyces_cerevisiae.R64-1-1.dna.toplevel.fa
export PATH_TO_RAW_UNDEMULTIPLEXED_FILE=/projects/RiboSeqAnalysis/riboprotma_MathildeGarcia/RT11_demultiplex.fastq
export SAMPLE_ARRAY=(/projects/RiboSeqAnalysis/riboprotma_MathildeGarcia/RT1_demultiplex.fastq /projects/RiboSeqAnalysis/riboprotma_MathildeGarcia/RT11_demultiplex.fastq /projects/RiboSeqAnalysis/riboprotma_MathildeGarcia/RT13_demultiplex.fastq /projects/RiboSeqAnalysis/riboprotma_MathildeGarcia/RT7_demultiplex.fastq)
export SAMPLE_INDEX_ARRAY=(NNNGGTTNN NNNAACCNN NNNTTAGNN NNNGGGANN)
export ADAPTER_SEQUENCE_THREE_PRIME=AGATCGGAAGAGGGGTTCAG
export CONDITION_ARRAY=(WT WT KO KO)
export STRANDED=yes
export DIFFERENTIAL_ANALYSIS_PACKAGE=EDGER
export AUTHOR=ExampleUser
export REFERENCE_CONDITION=WT