Cuffdiff and multiple gtf files?

[jwhite]

Hi,

I have been preparing cufflinks transcript.gtf files from mutant vs. wildtype strains of mice in order to do differential expression analysis. We have replicate samples from each. After cufflinks was run for each sample, I merge the gtf files with cuffmerge --as specified by the online documentation (http://cufflinks.cbcb.umd.edu/tutorial.html, "Differential analysis").

To run cuffdiff, only one gtf file argument is accepted, along with multiple bam files for each condition, and replicate. Are the cufflinks results from wildtype and mutant supposed to be combined into a single gtf file?

Joe

[id0]

Cufflinks includes a special tool cuffmerge specifically for this purpose.

Cufflinks includes a script called cuffmerge that you can use to merge together several Cufflinks assemblies. It handles also handles running Cuffcompare for you, and automatically filters a number of transfrags that are probably artfifacts. If you have a reference GTF file available, you can provide it to the script in order to gracefully merge novel isoforms and known isoforms and maximize overall assembly quality. The main purpose of this script is to make it easier to make an assembly GTF file suitable for use with Cuffdiff.

[csmatyi]

can cuffdiff be run to examine individual transcript results?

Hello everybody,

Can cuffdiff be run so as to do differential gene expression not on a gene by gene basis, as it does normally, but on a transcript basis?

In other words, cufflinks produces fpkm values for each transcript. Cuffmerge and cuffdiff then take these results and then merge them on a gene by gene basis.

Can cuffdiff be run so that it does the diff gene expression calculation for each transcript, not merging them into their corresponding gene?

Thanks!

[yueluo]

The output files named "isoforms*" contain information on transcript level.