<filename>configs/config_HuR_Penalva_L_01182017.human.py
GENOMES_DIR='/home/cmb-panasas2/skchoudh/genomes'
OUT_DIR = '/staging/as/skchoudh/rna/HuR_results/human/ribo-seq-06142017'
SRC_DIR = '/home/cmb-panasas2/skchoudh/github_projects/clip_seq_pipeline/scripts'
RAWDATA_DIR ='/home/cmb-06/as/skchoudh/dna/Oct_10_2016_HuR_Human_Mouse_Liver/Ribo-Seq-Human'
GENOME_BUILD = 'hg38'
GENOME_FASTA = GENOMES_DIR + '/' + GENOME_BUILD + '/fasta/'+ GENOME_BUILD+ '.fa'
STAR_INDEX = GENOMES_DIR + '/' + GENOME_BUILD + '/star_annotated'
GTF = GENOMES_DIR + '/' + GENOME_BUILD + '/annotation/' + 'gencode.v25.annotation.without_rRNA_tRNA.gtf'
GENE_NAMES = GENOMES_DIR + '/' + GENOME_BUILD + '/annotation/' + GENOME_BUILD+'_gene_names_stripped.tsv'
GTF_UTR = GENOMES_DIR + '/' + GENOME_BUILD + '/annotation/' + 'gencode.v25.gffutils.modifiedUTRs.gtf'
GENE_LENGTHS = GENOMES_DIR + '/' + GENOME_BUILD + '/annotation/' + 'gencode.v25.coding_lengths.tsv'  #+ GENOME_BUILD+'_gene_lengths.tsv'
DESIGN_FILE = RAWDATA_DIR + '/' + 'design.txt'
HTSEQ_STRANDED = 'yes'
FEATURECOUNTS_S = '-s 1'
GENE_BED = GENOMES_DIR + '/' + GENOME_BUILD + '/annotation/' + 'gencode.24.genes.bed'  #+ GENOME_BUILD+'_gene_lengths.tsv'
FEATURECOUNTS_T='CDS'
HTSEQ_MODE='intersection-strict'

<filename>configs/config_HuR_Penalva_L_01182017.human.py
GENOMES_DIR='/home/cmb-panasas2/skchoudh/genomes'
OUT_DIR = '/staging/as/skchoudh/rna/HuR_results/human/ribo-seq-06142017'
SRC_DIR = '/home/cmb-panasas2/skchoudh/github_projects/clip_seq_pipeline/scripts'
RAWDATA_DIR ='/home/cmb-06/as/skchoudh/dna/Oct_10_2016_HuR_Human_Mouse_Liver/Ribo-Seq-Human'
GENOME_BUILD = 'hg38'
GENOME_FASTA = GENOMES_DIR + '/' + GENOME_BUILD + '/fasta/'+ GENOME_BUILD+ '.fa'
STAR_INDEX = GENOMES_DIR + '/' + GENOME_BUILD + '/star_annotated'
GTF = GENOMES_DIR + '/' + GENOME_BUILD + '/annotation/' + 'gencode.v25.annotation.without_rRNA_tRNA.gtf'
GENE_NAMES = GENOMES_DIR + '/' + GENOME_BUILD + '/annotation/' + GENOME_BUILD+'_gene_names_stripped.tsv'
GTF_UTR = GENOMES_DIR + '/' + GENOME_BUILD + '/annotation/' + 'gencode.v25.gffutils.modifiedUTRs.gtf'
GENE_LENGTHS = GENOMES_DIR + '/' + GENOME_BUILD + '/annotation/' + 'gencode.v25.coding_lengths.tsv'  #+ GENOME_BUILD+'_gene_lengths.tsv'
DESIGN_FILE = RAWDATA_DIR + '/' + 'design.txt'
HTSEQ_STRANDED = 'yes'
FEATURECOUNTS_S = '-s 1'
GENE_BED = GENOMES_DIR + '/' + GENOME_BUILD + '/annotation/' + 'gencode.24.genes.bed'  #+ GENOME_BUILD+'_gene_lengths.tsv'
FEATURECOUNTS_T='CDS'
HTSEQ_MODE='intersection-strict'

#+ GENOME_BUILD+'_gene_lengths.tsv' #+ GENOME_BUILD+'_gene_lengths.tsv'