Difference between revisions of "Applications/Tophat"

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===Batch Job===
 +
<!-- Example from:  http://wiki.csi.cuny.edu/cunyhpc/index.php/TOPHAT -->
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<pre>
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#SBATCH -J tophatjob
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#SBATCH -N 1
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#SBATCH --ntasks-per-node 1
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#SBATCH -o %N.%j.%a.out
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#SBATCH -e %N.%j.%a.err
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#SBATCH -p compute
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#SBATCH --exclusive
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 +
module purge
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module load tophat/gcc/2.1.1
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 +
tophat -r 20 test_ref reads_1.fq reads_2.fq > tophat_mrna.out 2>&1
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</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]
  
{|
+
{{Modulepagenav}}
|style="width:5%; border-width: 0" | [[File:icon_home.png]]
 
|style="width:95%; border-width: 0" |
 
* [[Main_Page|Home]]
 
* [[Applications|Application support]]
 
* [[General|General]]
 
* [[Training|Training]]
 
* [[Programming|Programming support]]
 
|-
 
|}
 

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

Further Information





Modules | Main Page | Further Topics