LAST-PAIR-PROBS.PY(1) User Commands LAST-PAIR-PROBS.PY(1)
NAME
last-pair-probs.py - Read alignments of paired DNA reads to a genome
DESCRIPTION
Usage:
last-pair-probs.py --help last-pair-probs.py [options] alignments1 alignments2
Read alignments of paired DNA reads to a genome, and estimate the probability that each alignment represents the genomic source of the
read.
OPTIONS
-h, --help
show this help message and exit
-r, --rna
specifies that the reads are from potentially-spliced RNA
-m M, --mismap=M
don't write alignment pairs with mismap probability > M (default: 0.01)
-f BP, --fraglen=BP
mean fragment length in bp
-s BP, --sdev=BP
standard deviation of fragment length
-g BP, --genome=BP
haploid genome size in bp
-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)
last-pair-probs.py 199 May 2012 LAST-PAIR-PROBS.PY(1)
