Difference between revisions of "Applications/Tophat"
From HPC
m (Pysdlb moved page Tophat to Applications/Tophat without leaving a redirect) |
m |
||
| Line 33: | Line 33: | ||
With linkages to the following modules too: | With linkages to the following modules too: | ||
| + | * [[applications/Bowtie1|Bowtie1]] | ||
| + | * [[applications/Bowtie2|Bowtie2]] | ||
* [[applications/Cufflinks|Cufflinks]] | * [[applications/Cufflinks|Cufflinks]] | ||
* [[applications/Samtools|Samtools]] | * [[applications/Samtools|Samtools]] | ||
| − | + | ||
| − | |||
Revision as of 08:34, 6 April 2017
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 load tophat/gcc/2.1.1
Further Information
|