conf.txt

#PLEASE EDIT EACH VARIABLE BASED ON YOUR FILE SETTING!
#DON'T EDIT block title"--REF--", "--PBS--", "--BWA aln--", "--BWA samse--"
#Users may download REFERENCE files at http://bioinformatics.mdanderson.org/Software/PRADA/
#Set REFERENCE file paths according to your own settings. 

--REF--
compdb_fasta	=	/scratch/genomic_med/mtang1/PRADA/PRADA-ref-hg19/Ensembl64.transcriptome.plus.genome.fasta
compdb_map	=	/scratch/genomic_med/mtang1/PRADA/PRADA-ref-hg19/Ensembl64.transcriptome.plus.genome.map
genome_fasta	=	/scratch/genomic_med/mtang1/PRADA/PRADA-ref-hg19/Homo_sapiens_assembly19.fasta
genome_gtf	=	/scratch/genomic_med/mtang1/PRADA/PRADA-ref-hg19/Homo_sapiens.GRCh37.64.gtf
dbsnp_vcf	=	/scratch/genomic_med/mtang1/PRADA/PRADA-ref-hg19/dbsnp_135.b37.vcf
select_tx	=	/scratch/genomic_med/mtang1/PRADA/PRADA-ref-hg19/Ensembl64.selected.transcripts
feature_file	=	/scratch/genomic_med/mtang1/PRADA/PRADA-ref-hg19/Ensembl64.canonical.gene.exons.tab.txt
tx_seq_file	=	/scratch/genomic_med/mtang1/PRADA/PRADA-ref-hg19/Ensembl64.transcriptome.fasta
ref_anno	=	/scratch/genomic_med/mtang1/PRADA/PRADA-ref-hg19/Ensembl64.transcriptome.annotations
ref_map		=	/scratch/genomic_med/mtang1/PRADA/PRADA-ref-hg19/Ensembl64.transcriptome.formatted.map
ref_fasta	=	/scratch/genomic_med/mtang1/PRADA/PRADA-ref-hg19/Ensembl64.transcriptome.formatted.fasta
cds_file	=	/scratch/genomic_med/mtang1/PRADA/PRADA-ref-hg19/ensembl.hg19.cds.txt
txcat_file	=	/scratch/genomic_med/mtang1/PRADA/PRADA-ref-hg19/Ensembl64_primary_transcript.txt

--PBS--
-m = abe
-M = mtang1@mdanderson.org
-l = nodes=1:ppn=12,walltime=40:00:00,mem=30gb  #nodes and ppn are required

--BWA aln--
-t = 12					#This should be equal to the number of ppn

--BWA samse--
-n = 100