#!/usr/bin/perl

# directory with scripts
$script_directory="./";

# use or not to use cutadapt
$use_cutadapt="Yes";

# cutadapt executable, if it is not in system path program name should contain full path 
$cutadapt="cutadapt";

# parameters to be transferred to cutadapt program, edit -a for 3' adapters and -g for 5', -b for alternative for both 3' and 5'
$cutadapt_parameters="-a TCGTATGCCGTCTTCTGCTTG -g AATGATACGGCGACCACCGACAGGTTCAGAGTTCTACAGTCCGACGATC -b CGTACGCGGGTTTAAACGA -b CTCATCTTGGTCGTACGCGGAATAGTTTAAACTGT";

# bowtie executables, if it is not in system path program name should contain full path
$bowtie="bowtie";

