Read alignments of paired dna reads to a genome
last-pair-probs --help last-pair-probs [options] alignments1 alignments2
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.
-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)