Scroll to navigation
| LAST-SPLIT(1) |
User Commands |
LAST-SPLIT(1) |
NAME¶
last-split - Estimates "split" or "spliced" alignments.
SYNOPSIS¶
last-split [options] LAST-alignments.maf
DESCRIPTION¶
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.
OPTIONS¶
- -h, --help
- show this help message and exit
- -f, --format=FMT
- output format: MAF, MAF+ (default=MAF+)
- -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)
- -S, --sdev=SDEV
- standard deviation of ln[intron length] (default=1.7)
- -m, --mismap=PROB
- maximum mismap probability (default=0.01)
- -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
