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last-split - Online in the Cloud

Run last-split in OnWorks free hosting provider over Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

This is the command last-split that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator

PROGRAM:

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

-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[1000])

-n, --no-split
write original, not split, alignments

-v, --verbose
be verbose

-V, --version
show version information and exit

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