TopHat-SE
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TopHat (for single end reads) 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 identifies splice junctions between exons.
Quick Start
- To use TopHat-SE, import your data in fastq format.
- Resources: http://tophat.cbcb.umd.edu/
Version in DE makes use of a wrapper script developed by Sheldon McKay.
Test Data
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Test data for this app appears directly in the Discovery Environment in the Data window under _Community Data -> iplant_training -> intro_rna-seq. |
Input File(s)
Use hy5_rep1.fastq, hy5_rep2.fastq, WT_rep1.fastq and WT_rep2.fastq from the directory above as test input.
Parameters Used in App
When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below.
- Reference Genome: Arabidopsis thaliana (Ensembl 14)
- Reference Annotations: Arabidopsis thaliana (Ensembl 14)
All other parameters can be left at default values.
Output File(s)
Expect several directories as output. Example output directories and contents are located at Community Data-> iplant_training > intro_rna-seq >02_tophat
Tool Source for App
http://tophat.cbcb.umd.edu/downloads/tophat-2.0.7.tar.gz
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