This is the command last-pair-probs 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-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
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