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annotate pyPRADA_1.2/conf.txt @ 1:03815b87eb65 draft

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author siyuan
date Fri, 21 Feb 2014 18:08:37 -0500
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1 #PLEASE EDIT EACH VARIABLE BASED ON YOUR FILE SETTING!
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2 #DON'T EDIT block title"--REF--", "--PBS--", "--BWA aln--", "--BWA samse--"
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3 #Users may download REFERENCE files at http://bioinformatics.mdanderson.org/Software/PRADA/
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4 #Set REFERENCE file paths according to your own settings.
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6 --REF--
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7 compdb_fasta = /RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.transcriptome.plus.genome.fasta
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8 compdb_map = /RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.transcriptome.plus.genome.map
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9 genome_fasta = /RIS/home/verhaakgroup/PRADA/hg19broad/Homo_sapiens_assembly19.fasta
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10 genome_gtf = /RIS/home/verhaakgroup/PRADA/hg19broad/Homo_sapiens.GRCh37.64.gtf
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11 dbsnp_vcf = /RIS/home/verhaakgroup/PRADA/hg19broad/dbsnp_135.b37.vcf
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12 select_tx = /RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.selected.transcripts
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13 feature_file = /RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.canonical.gene.exons.tab.txt
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14 tx_seq_file = /RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.transcriptome.fasta
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15 ref_anno = /RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.transcriptome.annotations
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16 ref_map = /RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.transcriptome.formatted.map
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17 ref_fasta = /RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64.transcriptome.formatted.fasta
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18 cds_file = /RIS/home/verhaakgroup/PRADA/hg19broad/ensembl.hg19.cds.txt
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19 txcat_file = /RIS/home/verhaakgroup/PRADA/hg19broad/Ensembl64_primary_transcript.txt
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21 --PBS--
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22 -M = szheng2@mdanderson.org
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23 -q = long
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24 -l = nodes=1:ppn=12,walltime=120:00:00 #nodes and ppn are required
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26 --BWA aln--
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27 -t = 2 #This should be equal to the number of ppn
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29 --BWA samse--
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30 -n = 100
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