GMAP is a standalone program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models.
GSNAP can align both single- and paired-end reads as short as 14 nt and of arbitrarily long length. It can detect short- and long-distance splicing, including interchromosomal splicing, in individual reads, using probabilistic models or a database of known splice sites. Our program also permits SNP-tolerant alignment to a reference space of all possible combinations of major and minor alleles, and can align reads from bisulfite-treated DNA for the study of methylation state. This program is developed by Thomas D. Wu etc.
Please Note: the hg19 genome has been indexed for GMAP in:
/fdb/gmap
If you need other databases indexed for GMAP, please contact staff@helix.nih.govHow To Use
To set up the paths for gmap-gsnap, use the modules commands as in the example below:
[user@helix]$ module avail gmap-gsnap ------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles -------------------------------------------------------- gmap-gsnap/2012-01-11 gmap-gsnap/2012-04-27 gmap-gsnap/2012-05-24 gmap-gsnap/2012-06-06 gmap-gsnap/2012-07-20 gmap-gsnap/2012-03-21 gmap-gsnap/2012-05-07 gmap-gsnap/2012-06-02 gmap-gsnap/2012-06-20 gmap-gsnap/2012-07-20-v2 gmap-gsnap/2013-01-23 [user@helix]$ module load gmap-gsnap [user@helix]$ module list Currently Loaded Modulefiles: 1) gmap-gsnap/2013-01-23 [user@helix]$ module unload gmap-gsnap [user@helix]$ module load gmap-gsnap/2012-06-06 [user@helix]$ module list Currently Loaded Modulefiles: 1) gmap-gsnap/2012-06-06 [user@helix]$ module show gmap-gsnap ------------------------------------------------------------------ /usr/local/Modules/3.2.9/modulefiles/gmap-gsnap/2013-01-23: module-whatis Sets up gmap-gsnap 2013-01-23 prepend-path PATH /usr/local/apps/gmap-gsnap/2013-01-23/bin -------------------------------------------------------------------
Once you have the module loaded, you can type the gmap commands as in the example below:
For example, to map and align against hg19 :
To align against a given genomic segment:
