
RAWDATA_DIR = '/home/cmb-06/as/skchoudh/dna/Oct_10_2016_HuR_Human_Mouse_Liver/rna-seq/Penalva_L_08182016/mouse'
OUT_DIR = '/staging/as/skchoudh/rna/Oct_10_2016_HuR_Human_Mouse_Liver_ribocop_run_Jan2019/RNA-Seq-Mouse'
GENOME_FASTA = '/home/cmb-06/as/skchoudh/genomes/mm10/fasta/mm10.fa'
CHROM_SIZES = '/home/cmb-06/as/skchoudh/genomes/mm10/fasta/mm10.chrom.sizes'
STAR_INDEX = '/home/cmb-06/as/skchoudh/genomes/mm10/star_annotated'
GTF = '/home/cmb-06/as/skchoudh/genomes/mm10/annotation/gencode.vM11.annotation.gtf'
GENE_BED = '/home/cmb-06/as/skchoudh/github_projects/riboraptor/riboraptor/annotation/mm10/vM11/gene.bed.gz'
STAR_CODON_BED = '/home/cmb-06/as/skchoudh/github_projects/riboraptor/riboraptor/annotation/mm10/vM11/start_codon.bed.gz'
STOP_CODON_BED = '/home/cmb-06/as/skchoudh/github_projects/riboraptor/riboraptor/annotation/mm10/vM11/stop_codon.bed.gz'
CDS_BED = '/home/cmb-06/as/skchoudh/github_projects/riboraptor/riboraptor/annotation/mm10/vM11/cds.bed.gz'
UTR5_BED = '/home/cmb-06/as/skchoudh/github_projects/riboraptor/riboraptor/annotation/mm10/vM11/utr5.bed.gz'
UTR3_BED = '/home/cmb-06/as/skchoudh/github_projects/riboraptor/riboraptor/annotation/mm10/vM11/utr3.bed.gz'
INTRON_BED = '/home/cmb-06/as/skchoudh/github_projects/riboraptor/riboraptor/annotation/mm10/vM11/intron.bed.gz'
ORIENTATIONS = ['5prime', '3prime']
STRANDS = ['pos', 'neg', 'combined']
FRAGMENT_LENGTHS =  range(18, 39)
