Evolutionary conserved RNA structure prediction
Reads a set of maf files, realigns them with mafft, breaks them into windows, calculates stats, scans with SISSIz or RNAz, outputs bed coordonates of high-confidence predictions
Known issues: -Using MAFFT realignment causes certain jobs to hang when finished; this is likely an executor service problem
Usage: java -jar MafScanCcr.jar [options] -o output/directory -i input.maf (last parameter must be -i) Options: -bs int Block Size for splitting large MAF blocks (default 5000) -c int number of CPUs for calculations (default 4) -g int max gap percentage of sequences for 2D prediction (default 50) -mafft Realign with mafft-ginsi (slower) -ml int Max Length of MAF block for MAFFT realignment (default 10000) -s int step size (default 100) -v verbose (messy but detailed) output -w int window size (default 200)