Bowtie 1.2.2 build and map
This App takes any fasta file for a reference, builds the index and then maps reads to the index. Many options are allowed including mapping in colorspace.
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> bowtie.
Use e_coli_1000_1.fq and e_coli_1000_2.fq from the directory above as test input (query files). Use ecoli.fa as the 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 both fastq files above as inputs, the ecoli.fa file as a reference, and set the output format to SAM to obtain the results given in the example_data directory (e_coli_1000_pe.sam).
Expect a file named exactly as you name it as output. For the test case, the output file you will find in the example_data directory is named e_coli_1000_pe.sam.
Additional options can be entered (no spaces allowed) in the "other options" section. For mapping of colorspace reads against a colorspace reference, check the colorspace option.