Cuffdiff Output Explanation

[fongchun]

Hi all,

While trying to understand the output of the cuffdiff command I decided to create an image of what I believe cuffdiff is measuring. I wanted to share this image in case others had similar questions:

What Cuffdiff Measures

Feel free to comment on whether it is wrong or not. I am pretty sure I probably missed or misinterpreted something.

[dariober]

Hi- thanks for this fongchun. Once we are at it, a while ago I also made a diagram to visualize how the various output files from cuffdiff/cuffcompare relate to each other. See attached picture.

Big disclaimer: I haven't double checked whether it is entirely correct. It is deliberately not complete.

Any and all comments welcome.

Dario

[poojitharao]

Thanks very much fongchun for that image! Its very useful

[fongchun]

You're welcome. Glad it was helpful!

[fongchun]

I've updated the image (v2) to fix some errors in the biology and simplified it a bit. Enjoy!