Man page - last-split(1)

Packages contains this manual

Package:  last-align
apt-get install last-align

Manuals in package:
• maf-cut(1)
• lastdb(1)
• last-train(1)
• last-pair-probs(1)
• last-merge-batches(1)
• maf-join(1)
• lastal(1)
• fasta-nr(1)
• maf-swap(1)
• last-map-probs(1)
• maf-convert(1)
• last-postmask(1)
• fastq-interleave(1)
• maf-sort(1)
• last-split(1)
• last-dotplot(1)
Documentations in package:
• last-align

Manual

LAST-SPLIT

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

---

NAME

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

SYNOPSIS

last-split-plain [ 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+

-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

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