SNAP-Zoe-Teaching: Difference between revisions
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Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster. | Please refer to [[Running_Jobs_on_the_teaching_cluster]], [[Running_Jobs_on_the_teaching_cluster#Running_an_X-windows_application | Run X window Jobs]] and [[Running_Jobs_on_the_teaching_cluster#How_to_open_an_interactive_session | Run interactive Jobs]] for more details of running jobs at Teaching cluster. | ||
Here is an example of job submission command: | Here is an example of job submission command: | ||
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<pre class="gcommand"> | <pre class="gcommand"> | ||
ml SNAP-Zoe/20060728-foss-2016b | ml SNAP-Zoe/20060728-foss-2016b | ||
snap -help | |||
The general form of the snap command line is: | |||
snap <HMM file> <FASTA file> [options] | |||
HMM file: | |||
The most convenient way to specify the HMM file is by name. This requires | |||
that the ZOE environment variable is set. In this case, snap will look | |||
for the HMM file in $ZOE/HMM. You may also specify the HMM file by an | |||
explicit path. The following are equivalent if $ZOE is in /usr/local: | |||
snap C.elegans.hmm ... | |||
snap /usr/local/Zoe/HMM/C.elegans.hmm ... | |||
snap worm ... # there are a few convenient aliases in $ZOE/HMM | |||
FASTA file: | |||
If you have several sequences to analyze, it is more efficient to run | |||
snap on a concatenated FASTA file rather than separate runs on single | |||
sequence files. The seqeuence may be in a compressed format | |||
If sequences have been masked with lowercase letters, use -lcmask to | |||
prevent exons from appearing in masked DNA. | |||
Output: | |||
Annotation is reported to stdout in a non-standard format (ZFF). You can | |||
change to GFF or ACEDB with the -gff or -ace options. Proteins and | |||
transcripts are reported to FASTA files with the -aa and -tx options. | |||
External definitions: | |||
SNAP allows you to adjust the score of any sequence model at any point | |||
in a sequence. This behavior is invoked by giving a ZFF file to SNAP: | |||
snap <hmm> <sequence> -xdef <ZFF file> | |||
Each feature description uses the 'group' field to issue a command: | |||
SET set the score | |||
ADJ adjust the score up or down | |||
OK set non-cannonical scores | |||
>FOO | |||
Acceptor 120 120 + +50 . . . SET (sets an Acceptor to 50) | |||
Donor 212 212 + -20 . . . ADJ (lowers a Donor by -20) | |||
Inter 338 579 + -2 . . . ADJ (lowers Inter by -2 in a range) | |||
Coding 440 512 - +3 . . . ADJ (raises Coding by +3 in a range) | |||
Donor 625 638 + -5 . . . OK (sets range of odd Donors to -5) | |||
If the output has scrolled off your screen, try 'snap -help | more' | |||
</pre> | </pre> |
Latest revision as of 11:22, 15 August 2018
Category
Bioinformatics
Program On
Teaching
Version
20060728
Author / Distributor
Description
"SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser." More details are at SNAP-Zoe
Running Program
The last version of this application is at /usr/local/apps/eb/SNAP-Zoe/20060728-foss-2016b
To use this version, please load the module with
ml SNAP-Zoe/20060728-foss-2016b
Here is an example of a shell script, sub.sh, to run on the batch queue:
#!/bin/bash
#SBATCH --job-name=j_SNAP-Zoe
#SBATCH --partition=batch
#SBATCH --mail-type=ALL
#SBATCH --mail-user=username@uga.edu
#SBATCH --ntasks=1
#SBATCH --mem=10gb
#SBATCH --time=08:00:00
#SBATCH --output=SNAP-Zoe.%j.out
#SBATCH --error=SNAP-Zoe.%j.err
cd $SLURM_SUBMIT_DIR
ml SNAP-Zoe/20060728-foss-2016b
snap [options]
In the real submission script, at least all the above underlined values need to be reviewed or to be replaced by the proper values.
Please refer to Running_Jobs_on_the_teaching_cluster, Run X window Jobs and Run interactive Jobs for more details of running jobs at Teaching cluster.
Here is an example of job submission command:
sbatch ./sub.sh
Documentation
ml SNAP-Zoe/20060728-foss-2016b snap -help The general form of the snap command line is: snap <HMM file> <FASTA file> [options] HMM file: The most convenient way to specify the HMM file is by name. This requires that the ZOE environment variable is set. In this case, snap will look for the HMM file in $ZOE/HMM. You may also specify the HMM file by an explicit path. The following are equivalent if $ZOE is in /usr/local: snap C.elegans.hmm ... snap /usr/local/Zoe/HMM/C.elegans.hmm ... snap worm ... # there are a few convenient aliases in $ZOE/HMM FASTA file: If you have several sequences to analyze, it is more efficient to run snap on a concatenated FASTA file rather than separate runs on single sequence files. The seqeuence may be in a compressed format If sequences have been masked with lowercase letters, use -lcmask to prevent exons from appearing in masked DNA. Output: Annotation is reported to stdout in a non-standard format (ZFF). You can change to GFF or ACEDB with the -gff or -ace options. Proteins and transcripts are reported to FASTA files with the -aa and -tx options. External definitions: SNAP allows you to adjust the score of any sequence model at any point in a sequence. This behavior is invoked by giving a ZFF file to SNAP: snap <hmm> <sequence> -xdef <ZFF file> Each feature description uses the 'group' field to issue a command: SET set the score ADJ adjust the score up or down OK set non-cannonical scores >FOO Acceptor 120 120 + +50 . . . SET (sets an Acceptor to 50) Donor 212 212 + -20 . . . ADJ (lowers a Donor by -20) Inter 338 579 + -2 . . . ADJ (lowers Inter by -2 in a range) Coding 440 512 - +3 . . . ADJ (raises Coding by +3 in a range) Donor 625 638 + -5 . . . OK (sets range of odd Donors to -5) If the output has scrolled off your screen, try 'snap -help | more'
Installation
Source code is obtained from SNAP-Zoe
System
64-bit Linux