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exonpairs - SNAP module exonpairs

EXONPAIRS(1) User Commands EXONPAIRS(1)

NAME

exonpairs - SNAP module exonpairs

SYNOPSIS

exonpairs [ options] <HMM file> <FASTA file> [ options]

OPTIONS

-min-intron <int>
minimum Intron length [30]
-max-intron <int>
maximum Intron length [10000]
-einit-length <int>
minimum Einit length in bp [10]
-eterm-length <int>
minimum Eterm length in bp [10]
-exon-length <int>
minimum Exon length in bp [30]
-intron-score <float> minimum Intron score in bits [-5]
-einit-score <float>
minimum Einit score in bits [-5]
-eterm-score <float>
minimum Eterm score in bits [-5]
-exon-score <float>
minimum Exon score in bits [-5]
-pair-score <float>
minimum pair score (exon-intron-exon) [10]
-flank-length <int>
length of flanking sequence per exon [20]
-lcmask
treat lowercase as N
October 2013 exonpairs 2010-07-28