hmm-assembler.pl(1) SNAP module hmm-assembler.pl

SYNOPSIS

hmm-assembler.pl [-OPTIONS [-MORE_OPTIONS]] [--] [PROGRAM_ARG1 ...]

OPTIONS

The following single-character options are accepted:

With arguments: -i -e -A -D -M -S -C -I -N -a -3 -5 -Z -c

Boolean (without arguments): -r -o -x -p -t -1

Options may be merged together. -- stops processing of options. Space is not required between options and their arguments.

Options:

-i
<length> [500]
-e
<length> [1000]
-A
<order:length> [0:30]
-D
<order:length> [0:9]
-M
<order:length> [0:15]
-S
<order:length> [0:9]
-C
<order> [4]
-I
<order> [4]
-N
<order> [4]
-3
<order:length> [] include 3'UTR model, requires -a
-a
<order:length> [] include PolyA model, requires -3
-5
<order:length> [] include 5'UTR moel, requires -p
-p
include generic promoter model, requires -5
-r
include generic repeat model
-o
include reverse ORF model
-x
use explicit duration intron model
-t
include C.elegans trans-splicing, requires -p, -5
-Z
<clade> sets clade-specific values (worm, fly, plant)
-1
single gene model
-c <score>
include GC-AG splice donor model