...
- To use Cuffdiff2 with JS option,
- import your
- BAM files and your GTF file
Resources:http://
...
...
umd.edu/, http://cufflinks.cbcb.umd.edu/tutorial.html and http://cufflinks.cbcb.umd.edu/howitworks.html#hdif
Test Data
...
...
...
Input File(s)
Use TerriblyIncomprehensible.txt and HorriblyWritten.txt 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.Use either the "
- Default
...
- parameters
...
- Default parameters only, no further configuration needed.
OR
- Use these parameters within the DE app interface:
- parameter name - value/setting
- parameter name - value/setting
- only, and WT vs hy5 sample names
Output File(s)
Expect a text file named after the input files as output. For the test case, the output file you will find in the example_data directory is named BeautifulProse.txt.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.
Tool Source for App
- http
- replace.with.URL.for.tool.org