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TopHat Aligner for Single-End Illumina Reads

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 Single-End Illumina Reads is targeted to work with single-end alignments only.

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

All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > tophat_single_end_illumina_reads

Input File(s)

Use SRR070572_hy5.fastq (2.6 G) as test data.

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 - Arabidopsis thaliana (Col-0 thale cress) v10
    • Leave other parameters in their default settings.

Output File(s)

  1. Expect a BAM (binary SAM) file named after the input file as output. In the case of the test data, it will be SRR070572_hy5.fastq.tophat.bam
  2. Expect a set of BED files, which will in the case of the test case, have no entries.
    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.