TraFiC_candReads.pl - Find candidate reads for transposon or viral detection
TraFiC_candReads.pl [-h] -o /some/path/ -i sample.bam -i lane.ump.bam ...
Required options: --input (-i) Define at least once Other options: --output (-o) Output written to specified folder as candidates.fa [.] --chr (-c) Process just this chromosome/contig - Output will be prefixed with seq name - Additional output files of <chr>.o1.fa and <chr>.o2.fa generated - handling these is out of the scope of this help. --help (-h) This message Examples: TraFiC_candReads.pl -o $HOME/trafic/COLO-829 -i COLO-829.bam