Difference between revisions of "Gmap"
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*{{#var:app}} | *{{#var:app}} | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
* HPC_GMAP_BIN - executable directory. | * HPC_GMAP_BIN - executable directory. | ||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
| − | The default shared Genome Database location is <code>/ | + | The default shared Genome Database location is <code>/data/reference/gmap</code>. If you are a part of a group that's using a large Genome Database you're welcome to put the shared data into the shared Genome Database location. This is, of course, not necessary for custom databases that can be passed to the gmap with "-D" and "-d" command line switches. |
| + | |||
| + | If you are using an older gmap module the reference directory path could be wrong in which case you can specify the path with the '-D' argument. | ||
| + | |||
| + | Make sure to request two additional processors by increasing the "ppn" in the job script accordingly when running with the "-t X" argument to enable multi-threaded execution. When "-t" is used Gmap will create two more processes than the number of threads set with "-t", which will interfere with other people's jobs on the server gmap is running on and could result in the offending user's account being disabled. | ||
|}} | |}} | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Revision as of 19:19, 11 February 2021
Description
GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences, and GSNAP: Genomic Short-read Nucleotide Alignment Program
Required Modules
Serial
- gmap
System Variables
- HPC_GMAP_DIR - installation directory
- HPC_GMAP_BIN - executable directory.
How To Run
The default shared Genome Database location is /data/reference/gmap. If you are a part of a group that's using a large Genome Database you're welcome to put the shared data into the shared Genome Database location. This is, of course, not necessary for custom databases that can be passed to the gmap with "-D" and "-d" command line switches.
If you are using an older gmap module the reference directory path could be wrong in which case you can specify the path with the '-D' argument.
Make sure to request two additional processors by increasing the "ppn" in the job script accordingly when running with the "-t X" argument to enable multi-threaded execution. When "-t" is used Gmap will create two more processes than the number of threads set with "-t", which will interfere with other people's jobs on the server gmap is running on and could result in the offending user's account being disabled.
Citation
If you publish research that uses gmap you have to cite it as follows:
Thomas D. Wu and Colin K. Watanabe GMAP: a genomic mapping and alignment program for mRNA and EST sequences Bioinformatics 2005 21:1859-1875
Thomas D. Wu and Serban Nacu Fast and SNP-tolerant detection of complex variants and splicing in short reads Bioinformatics 2010 26:873-881