TophatFusion on Helix
TopHat-Fusion is an enhanced version of TopHat with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome.
/usr/local/tophatfusion/binThe executables for TopHatFusion, Samtools and Bowtie have to be added to your path. This is most easily done by using the modules commands as in the example below:
biowulf% module load tophatfusion biowulf% module list Currently Loaded Modulefiles: 1) tophatfusion
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 transcript annotation files called iGenomes. These files can be used with TopHat and Cufflinks to quickly perform expression analysis and gene discovery. The annotation files are augmented with the tss_id and p_id GTF attributes that Cufflinks needs to perform differential splic,ing, CDS output, and promoter user analysis. Bowtie indexes can be found under the 'Sequence' subdirectory of each organism in iGenomes.
How To Use
helix$ module load tophatfusion helix$ tophat-fusion -o tophat_MCF7 -p 8 --allow-indels --no-coverage-search -r 0 --mate-std-dev 80 --fusion-min-dist 100000 --fusion-anchor-length 13 \ /fdb/igenomes/Homo_sapiens/UCSC/hg19/Sequence/BowtieIndex/genome.fa \ SRR064286_1.fastq SRR064286_2.fastq