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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:


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

Further Information