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This application is being archived. Workflow described below for example is no longer valid due to update of genome services.

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 identifies splice junctions between exons. This application, TopHat Aligner for Paired-End Illumina Reads is targeted to work with paired-end alignments.

Quick Start

  • To use TopHat, upload your data in FASTQ format, choose a reference genome, and select parameters as appropriate. Results will be a BAM file and several accessory files.
  • Resources: TopHat documentation

Test Data

Input File(s)

Use 5M_SRR040820_1.fastq (1.1 G) http://mirrors.iplantcollaborative.org/example_data/tophat_aligner_paired_end_illumina_reads/5M_SRR040820_1.fastq and 5M_SRR040820_2.fastq (1.2 G) http://mirrors.iplantcollaborative.org/example_data/tophat_aligner_paired_end_illumina_reads/5M_SRR040820_2.fastq as test data. Import from URL to get the data into your Discovery Environment account.

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.

  • Use these parameters within the DE app interface:
    • Select a reference genome - Eucalyptus grandis (BRASUZ1) v1
    • Leave other parameters in their default settings.

Output File(s)

  1. Expect a BAM (binary SAM) file given the default tophat output name: accepted_hits.bam
  2. Expect a set of BED files containing junctions, insertions, and deletions.
    1. deletions.bed
    2. insertions.bed
    3. junctions.bed

Tool Source for App

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This app has been deprecated and is no longer available. Please use a Hisat2 app in the DE, which more efficiently and accurately provides the same core functionality (i.e., spliced alignment of RNA-Seq reads). If you cannot find a suitable replacement, please contact CyVerse Support at support@cyverse.org.