TopHat on Helix
TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons.
TopHat is a collaborative effort between the University of Maryland Center for Bioinformatics and Computational Biology and the University of California, Berkeley Departments of Mathematics and Molecular and Cell Biology.
/usr/local/tophat/binIndex files can be accessed /fdb/igenomes/YourSelectionHere
The iGenomes is available on helix/biowulf in /fdb/igenomes.
Illumina has provided the RNA-Seq user community with a set of genome sequence indexes (including Bowtie indexes) as well as GTF t ranscript annotation files called iGenomes. These files can be used with TopHat and Cufflinks to quickly perform expression analys is and gene discovery. The annotation files are augmented with the tss_id and p_id GTF attributes that Cufflinks needs to perform differential splicing, CDS output, and promoter user analysis.
How To UseThe Tophat and Bowtie executables need to be added to your path. The easiest way to do this is by using the modules commands, as in the example below.
[user@helix]$ module avail tophat ----------------- /usr/local/Modules/3.2.9/modulefiles ----------------------------- tophat/2.04/bowtie tophat/2.05/bowtie tophat/2.06/bowtie tophat/2.04/bowtie2 tophat/2.05/bowtie2 tophat/2.06/bowtie2(default) [user@helix]$ module load tophat (loads the default version) [user@helix]$ module list Currently Loaded Modulefiles: 1) tophat/2.06/bowtie2 [user@helix]$ module unload tophat [user@helix]$ module load tophat/2.05/bowtie (loads a specific version) [user@helix]$ module list Currently Loaded Modulefiles: 1) tophat/2.05/bowtie
Example files below can be copied from /usr/local/src/tophat/test_data.tar.gz
helix% cd /home/username/tophat/test_data helix% module load tophat helix% tophat -r 20 test_ref reads_1.fq reads_2.fq