exonpairs(1)
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
