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An HPC version of the GSNAP splice alignment application.
- To use GSNAP 121212, import your data in fastq or fasta format, all files in a single directory.
- Resources: https://github.com/julian-gehring/GMAP-GSNAP
Use the ecSeqs directory from the directory above as test input. Use the E coli genome (in the gsnap directory) as a reference.
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 Ecoli as the index name. Otherwise use defaults completely.
Expect a .sam file for each of the input files as output. For the test case, the output files will each be named "inputfilename".sam.