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
