BAM to Counts (named outputs)

Test Data

Input File(s)

Use hy5_rep1.bam and annotation.gff 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 file(s) to get the output provided in the next section below.

• Default parameters and set feature to count to gene_name.

Output File(s)

Expect a tab-delimited file as output. For the test case, the output file you will find in the example_data directory is named hy5testout.

Tool Source for App

• http://www.iplantcollaborative.org/learning-center/discovery-environment/de-003-characterizing-differential-expression-rna-seq