Applications/Tophat

Application Details

• Description: 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.
• Version: 2.1.1 (compiled with gcc)
• Module: module tophat/gcc/2.1.1
• Licence: open source and freely available under the Artistic license

Usage Areas

Tophat has the following commands available:

• bam_merge
• bam2fastx
• bed_to_juncs
• contig_to_chr_coords
• fix_map_ordering
• gtf_juncs
• gtf_to_fasta
• juncs_db
• long_spanning_reads
• map2gtf
• prep_reads
• sam_juncs
• samtools_0.1.18
• segment_juncs
• sra_to_solid
• tophat
• tophat_reports
• tophat2
• tophat-fusion-post

With linkages to the following modules too:

• Bowtie1
• Bowtie2
• Cufflinks
• Samtools

Module

[username@login01 ~]$ module add tophat/gcc/2.1.1

Batch Job

#SBATCH -J tophatjob
#SBATCH -N 1
#SBATCH --ntasks-per-node 1
#SBATCH -o %N.%j.%a.out
#SBATCH -e %N.%j.%a.err
#SBATCH -p compute
#SBATCH --exclusive

module purge
module load tophat/gcc/2.1.1

tophat -r 20 test_ref reads_1.fq reads_2.fq > tophat_mrna.out 2>&1

Further Information

• https://ccb.jhu.edu/software/tophat/index.shtml

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