> I got the normalized values (FPKM) from cufflinks. And I want to get relative
> reads counts. How can I do that?
It's not clear to me what you're looking for. FPKM is a normalized read count
metric where the F stands for fragment, which is a single read (or half of a
> Another question: how does cufflinks handle isoform genes while calculating
> the reads counts? Or what papers can help me understand this?
Expectation maximization is used to probabilistically assign reads to isoforms.
See the Cufflinks documentation for details and paper links:
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at: