Items in PURPLE and links are the things you must modify. Change PURPLE items to BLACK when you save your page.

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CuffDiff 

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Cuffdiff used GTF2/GFF3 annotatiuon files of transcripts, along with two or more SAM/BAM files containing the read alignments. It compares expression levels at the level of transcripts, primary transcripts, and genes.

Cuffdiff

Community rating: ?????

Cuffdiff used performs differential transcript abundance analysis for two or more RNA-Seq samples.

Cuffdiff uses GTF2/GFF3 annotatiuon annotation files of transcripts, along with two or more SAM/BAM files containing the read alignments. It compares expression levels at the level of transcripts, primary transcripts, and genes.

Quick Start

• To use CuffDiffuse Cuffdiff2, import your data in ___ format.your BAM files and your GTF file
• Resources: http://replacecufflinks.cbcb.with.URL.for.tool.documentation.from.the.tool.source.orgumd.edu/, http://cufflinks.cbcb.umd.edu/tutorial.html and http://cufflinks.cbcb.umd.edu/howitworks.html#hdif

Test Data

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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..." section OR fill in the "Use these parameters..." section. Delete the unused section and the OR. Then, delete this note.

• Default parameters only, no further configuration needed.

OR

• Use these parameters within the DE app interface:
• parameter name - value/setting
parameter name - value/settingand 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

• httphttps://replace.with.URL.for.tool.orggithub.com/cole-trapnell-lab/cufflinks