Scroll to navigation

LAST-SPLIT(1) User Commands LAST-SPLIT(1)


last-split - Estimates "split" or "spliced" alignments.


last-split-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.


show this help message and exit
output format: MAF, MAF+
reverse the roles of the 2 sequences in each alignment
lastdb genome name
RNA direction: 0=reverse, 1=forward, 2=mixed (default: 1)
cis-splice probability per base (default: 0.004)
trans-splice probability per base (default: 1e-05)
mean of ln[intron length] (default: 7.0)
standard deviation of ln[intron length] (default: 1.7)
maximum mismap probability (default: 1.0)
minimum alignment score (default: e OR e+t*ln[100])
write original, not split, alignments
maximum memory (default: 8T for split, 8G for spliced)
be verbose
show version information and exit
January 2023 last-split 1420