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)
Check Out this Related Man Page
LASTAL(1) User Commands LASTAL(1)NAME
lastal - genome-scale comparison of biological sequences
SYNOPSIS
lastal [options] lastdb-name fasta-sequence-file(s)
DESCRIPTION
Find local sequence alignments.
Score options (default settings): -r: match score (DNA: 1, protein: blosum62, 0<Q<5: 6) -q: mismatch cost (DNA: 1, protein: blosum62,
0<Q<5: 18) -p: file for residue pair scores -a: gap existence cost (DNA: 7, protein: 11, 0<Q<5: 21) -b: gap extension cost (DNA: 1, pro-
tein: 2, 0<Q<5: 9) -c: unaligned residue pair cost (100000) -F: frameshift cost (off) -x: maximum score drop for gapped alignments
(max[y, a+b*20]) -y: maximum score drop for gapless alignments (t*10) -z: maximum score drop for final gapped alignments (x) -d: minimum
score for gapless alignments (e*3/5) -e: minimum score for gapped alignments (DNA: 40, protein: 100, 0<Q<5: 180)
Cosmetic options (default settings): -h: show all options and their default settings -v: be verbose: write messages about what lastal is
doing -o: output file -f: output format: 0=tabular, 1=maf (1)
Miscellaneous options (default settings): -s: strand: 0=reverse, 1=forward, 2=both (2 for DNA, 1 for protein) -m: maximum multiplicity for
initial matches (10) -l: minimum length for initial matches (1) -n: maximum number of gapless alignments per query position (infinity) -k:
step-size along the query sequence (1) -i: query batch size (1 MiB if Q>0, else 16 MiB if j=0, else 128 MiB) -u: mask lowercase during
extensions: 0=never, 1=gapless,
2=gapless+gapped but not final, 3=always (2 if lastdb -c and Q<5, else 0)
-w: supress repeats inside exact matches, offset by this distance or less (1000) -G: genetic code file -t: 'temperature' for calculating
probabilities (1/lambda) -g: 'gamma' parameter for gamma-centroid and LAMA (1) -j: output type: 0=match counts, 1=gapless, 2=redundant
gapped, 3=gapped,
4=column ambiguity estimates, 5=gamma-centroid, 6=LAMA (3)
-Q: input format: 0=fasta, 1=fastq-sanger, 2=fastq-solexa, 3=fastq-illumina,
4=prb, 5=PSSM (0)
REPORTING BUGS
Report bugs to: last (ATmark) cbrc (dot) jp
LAST home page: http://last.cbrc.jp/
lastal 199 May 2012 LASTAL(1)