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LAST-PAIR-PROBS(1) User Commands LAST-PAIR-PROBS(1)

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

show this help message and exit
assume the reads are from potentially-spliced RNA
just estimate the distribution of distances
don't write alignments with mismap probability > M (default: 0.01)
mean distance in bp
standard deviation of distance
prior probability of disjoint mapping (default: 0.02 if -r, else 0.01)
specifies that chromosome CHROM is circular (default: chrM)
show program's version number and exit
December 2015 last-pair-probs 712