TopHat is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the short read aligner Bowtie and analyzes the mapping results to identify splice junctions between exons. TopHat2 provides an interface to TopHat version 2.1.x for both single-end and paired-end reads (library type fr_unstranded). By default, Bowtie 2.2.5 is used as the alignment engine.
Versions - tophat-2.1.0 and tophat-2.1.1 (latest version)
Test Data (for both 2.1.0 and 2.1.1)
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Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> tophat2-PE |
Input File(s)
Use "e_coli_1000_1.fq" file in the left_reads folder as PE1 and "e_coli_1000_2.fq" file in the right_reads folder as PE2. For the custom reference use "NC_010473.fa" in the reference folder. Alternately you could just either of the PE1 or PE2 read and the app still works
Parameters Used in App
When the app is run in the Discovery Environment, use the default parameters with the above input file(s) to get the output provided in the next section below.
Output File(s)
- log folder
- tophat_folder
- accepted_hits.bam
- align_summary.txt
- deletions.bed
- insertions.bed
- junctions.bed
- unmapped.bam
- prep_reads.info
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. |