Screens fastq files against specific databases for contaminants or alternate sequences.
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> fastq_screen
Use testdata.fq and the genomes directory from the directory above as test input. For running your own data, the bowtie2 index(es) must be contained in a directory named genomes, and the indexes must be named genome1, genome2, genome3 etc.
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.
- Default parameters only, no further configuration needed.
Expect a text file named after the input files as output. For the test case, the output files you will find in the example_data directory are named testdata_screen.png and testdata_screen.txt.