Man page - last-pair-probs(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-PAIR-PROBS

NAME
SYNOPSIS
DESCRIPTION
OPTIONS

---

NAME

last-pair-probs - Read alignments of paired DNA reads to a genome, and do estimations

SYNOPSIS

last-pair-probs [options] interleaved-alignments

last-pair-probs [options] alignments1 alignments2

DESCRIPTION

Read alignments of paired DNA reads to a genome, and: (1) estimate the distribution of distances between paired reads, (2) estimate the probability that each alignment represents the genomic source of the read.

OPTIONS

-h , --help

show this help message and exit

-r , --rna

assume the reads are from potentially-spliced RNA

-e , --estdist

just estimate the distribution of distances

-m M, --mismap = M

don’t write alignments with mismap probability > M (default: 0.01)

-f BP, --fraglen = BP

mean distance in bp

-s BP, --sdev = BP

standard deviation of distance

-d PROB, --disjoint = PROB

prior probability of disjoint mapping (default: 0.02 if -r , else 0.01)

-c CHROM, --circular = CHROM

specifies that chromosome CHROM is circular (default: chrM)

-V , --version

show program’s version number and exit

---