NAME¶
hmm-assembler.pl - 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