REF_GENOME=/data2/bsi/RandD/s112328.mRNA-SEQ_Zebrafish/Zv9/Reference/danRer7ChrM.fa
BOWTIE_REF=/data2/bsi/RandD/s112328.mRNA-SEQ_Zebrafish/Zv9/Reference/danRer7ChrM
MIRBASE_HAIRPIN=/data4/bsi/refdata/mirbase/v18/hairpin.dre.dna.fa
MIRBASE_MATURE=/data4/bsi/refdata/mirbase/v18/mature.dre.dna.fa

SCRIPT_PATH=/projects/bsi/bictools/scripts/miRNA/trunk/
MIRDEEP2_PATH=/projects/bsi/bictools/apps/miRNA/mirdeep/2.0.0.5/
BOWTIE_PATH=/projects/bsi/bictools/apps/alignment/bowtie/0.12.7/
RANDFOLD_PATH=/projects/bsi/bictools/apps/miRNA/mirdeep/2.0.0.5/essentials/randfold-2.0/
SQUID_PATH=/projects/bsi/bictools/apps/miRNA/mirdeep/2.0.0.5/essentials/squid-1.9g/
VIENNA_PATH=/projects/bsi/bictools/apps/miRNA/mirdeep/2.0.0.5/essentials/ViennaRNA-1.8.4/install_dir/bin/
PDFAPI2_PM_PATH=/projects/bsi/bictools/apps/miRNA/mirdeep/2.0.0.5/lib/lib/perl5/
JAVA_PATH=/usr/java/latest/bin/
PICARD_PATH=/projects/bsi/bictools/apps/alignment/picard/1.67/
FASTQC_PATH=/projects/bsi/bictools/apps/qc/FastQC
CUTADAPT_PATH=/projects/bsi/bictools/apps/miRNA/cutadapt/0.9.5/
SAMTOOLS_PATH=/projects/bsi/bictools/apps/alignment/samtools/samtools-0.1.12a/
BEDTOOLS_PATH=/projects/bsi/bictools/apps/misc/BEDTools/2.15.0/bin/

#ADAPTER_SEQS=TCGTATGCCGTCTTCTGCTTG
#ADAPTER_SEQS=AATCTCGTATGCCGTCTTCTGCTTGC
ADAPTER_SEQS=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC:GTGACTGGAGTTCAGACGTGTGCTCTTCCGATCT:GATCTACACGTTCAGAGTTCTACAGTCCGACGATC:GATCGTCGGACTGTAGAACTCTGAACGTGTAGATC:TCGTATGCCGTCTTCTGCTTG
UCSC_SPECIES=dre
STAR_NOTATION=NO
BOWTIE_THREADS=4
BOWTIE_MULTIMAP_MAX=10
BOWTIE_MISMATCHES_IN_SEED=1
SORTSAM_MAX_READS_IN_MEM=1800000
CUTADAPT_MIN_OVERLAP=3
CUTADAPT_MIN_LENGTH=17
