exonpairs1
Snap module exonpairs
Usage
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