cufflinks cummeRbund set condition

[Jetse]

Hello everyone,

I'm using the pipeline of tophat -> cufflinks -> cummeRbund.
Now I'm using cummeRbund, but my conditions are q1 and q2...
My read_groups.info looks like this:

file	condition	replicate_num	total_mass	norm_mass	internal_scale	external_scale
polymin1.merged.bam	q1	0	6.16223e+06	1.56554e+07	0.920662	1
polyplus1.merged.bam	q2	0	7.87942e+06	1.56554e+07	1.09299	1

How and in which step I can change this condition?

Is there an option in cufflinks to set this condition?
Or is there an option in cummeRbund to change this condition (with use of the filename)?
I want to have the condition the same as the part before the .merged.bam...

[lgoff]

You can use the -L argument to cuffdiff to add labels to your conditions...