TraFic_cluster.pl - Generate files suitable for input to cluster discovery
TraFic_cluster.pl [-h] -o /some/path/ -r %.out -f %.fa
Required options: --rm (-r) Repeat masker *.out files --fa (-f) Modified fasta format originally supplied to repeat masker NOTE: Both can be defined once with/without wildcard % or multiple times Other options: --output (-o) Output written to specified folder (current working directory otherwise): - pos_hits.txt - neg_hits.txt - pos_clusters.txt - neg_clusters.txt --min (-m) Minimum number of reads required to emit a cluster. [5] --paired (-p) Excludes single end mapped Alu from clustering --help (-h) This message Examples: TraFic_cluster.pl -o $HOME/trafic -r COLO-829.%.fa.out -f COLO-829.fa