A simple script that calls piRNA clusters given a bed2 file and a file containing the length of each chromosome.
Usage: pirna_cluster_caller.py -f FILE -g GENOME [-u]
Given a fasta file, this script outputs two columns, which is suitable for line-oriented programs.
Given a bed12 format file, this script will output the bed12 describing left and right flanking regions of the splice site.
Given the scores from pps_simple.py, this script will plot them.
Given a bed12 file for just one gene, this script outputs the gene plot (for all_mappers, uniq_mappers)
Usage: bed12_to_depth.sh one_gene.bed12 gene.name gene.length n_all_mappers n_uniq_mapper