Cuffdiff2
Cuffdiff2
Cuffdiff performs differential transcript abundance analysis for two or more RNA-Seq samples.
App Creator
Roger Barthelson
Quick Start
- To use Cuffdiff2, import your BAM files and your GTF file
- Resources: http://cole-trapnell-lab.github.io/cufflinks/
Test Data
Test data for this app appears directly in the Discovery Environment in the Data window under Community Data -> iplantcollaborative -> example_data -> cuffdiff
Input File(s)
Use the following files from the directory above as test input:
hy5_rep1.bam
hy5_rep2.bam
merged_with_ref_ids.gtf
WT_rep1.bam
WT_rep2.bam
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, and WT vs hy5 sample names
Output File(s)
Expect a series of files describing the expression for genes and transcripts as output in a cuffdiff_out directory and a series of sorted files of significantly features that have significantly different expression in the sorted_data directory.