Difference between revisions of "Applications/Tophat"
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(Created page with "==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-throug...") |
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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]] | ||
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<pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | <pre style="background-color: #000000; color: white; border: 2px solid black; font-family: monospace, sans-serif;"> | ||
| − | [username@login01 ~]$ module | + | [username@login01 ~]$ module add tophat/gcc/2.1.1 |
</pre> | </pre> | ||
| + | ===Batch Job=== | ||
| + | <!-- Example from: http://wiki.csi.cuny.edu/cunyhpc/index.php/TOPHAT --> | ||
| + | <pre> | ||
| + | #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 | ||
| + | |||
| + | </pre> | ||
==Further Information== | ==Further Information== | ||
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* [https://ccb.jhu.edu/software/tophat/index.shtml https://ccb.jhu.edu/software/tophat/index.shtml] | * [https://ccb.jhu.edu/software/tophat/index.shtml https://ccb.jhu.edu/software/tophat/index.shtml] | ||
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Latest revision as of 10:58, 17 November 2022
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
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