last-split5 - Estimates "split" or "spliced"
alignments.
last-split5-plain [options]
LAST-alignments.maf
Read alignments of query sequences to a genome, and estimate the
genomic source of each part of each query, allowing different parts of one
query to come from different parts of the genome.
- -h, --help
- show this help message and exit
- -f,
--format=FMT
- output format: MAF, MAF+
- -r, --reverse
- reverse the roles of the 2 sequences in each alignment
- -g,
--genome=NAME
- lastdb genome name
- -d,
--direction=D
- RNA direction: 0=reverse, 1=forward, 2=mixed (default: 1)
- -c,
--cis=PROB
- cis-splice probability per base (default: 0.004)
- -t,
--trans=PROB
- trans-splice probability per base (default: 1e-05)
- -M,
--mean=MEAN
- mean of ln[intron length] (default: 7.0)
- -S,
--sdev=SDEV
- standard deviation of ln[intron length] (default: 1.7)
- -m,
--mismap=PROB
- maximum mismap probability (default: 1.0)
- -s,
--score=INT
- minimum alignment score (default: e OR e+t*ln[100])
- -n,
--no-split
- write original, not split, alignments
- -b,
--bytes=B
- maximum memory (default: 8T for split, 8G for spliced)
- -v, --verbose
- be verbose
- -V, --version
- show version information and exit