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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. The index is saved in tar.gz form. Many options are allowed including mapping in colorspace. This is the earlier version of Bowtie-2, which is faster. But Bowtie can be used for mapping reads to transcripts for use with RSEM. Bowtie2 can only be used with the newest versions of RSEM and requires special settings. 

Quick Start

Test Data


Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> bowtie.

Input File(s)

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).

Output File(s)

Expect a file named exactly as you name it (Hits file) as output. For the test case, the output file you will find in the example_data directory is named e_coli_1000_pe.sam.

Advanced Use

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. To save time and resources, use the 'Bowtie-Map-Only' App with the indexed reference created with Bowtie-Build-and-Map. 

Tool Source for App