Difference between revisions of "Applications/Tophat"
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* [[General|General]] | * [[General|General]] | ||
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* [[Programming|Programming support]] | * [[Programming|Programming support]] | ||
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Revision as of 13:50, 24 May 2019
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:
Module
[username@login01 ~]$ module add tophat/gcc/2.1.1