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TopHat 2.0.11 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. THIS APP FOR TOPHAT IS DESIGNED TO WORK AS PART OF THE HTPROCESS PIPELINE/SUITE OF TOOLS
- To use HTProcess-Tophat-2.0.11, import your HTProcess_Reads_T1.
- Resources: http://tophat.cbcb.umd.edu/manual.shtml
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> htprocess1 > HTProcess_Trimmomatic
Use 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 directory to get the output provided in the Community Data -> iplantcollaborative -> example_data -> htprocess1 -> HTProcess_Tophat2 directory.
- Default parameters only, except set segment length to 25 bp.
Expect a directory named HTProcess_BAM_control as output with sample data. The name control comes from the entry made into HTProcess_Fastqc originally for the condition parameter for the read library.
Tool Source for App
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 email@example.com.