I have a few questions regarding RNA-seq data analysis. I want to compare
transcriptome profile of a bacterium between 5 time points, and for each
time point I have three biological replicates.
Right now I have each of the replicates' sequences aligned with Bowtie and
assembled transcripts generates using Cufflinks. I understand that if I am
just comparing two time points (if each of time point has only one sample,
no replicate) I just need to cuffmerge the two time points and cuffdiff the
My question is, if I need to compare between 5 time points, should I do
And also, how should I include three biological replicates for each time
point? I can only find 'include replicates' in Cuffdiff. Could you check is
the following methodology correct?
let's say I have samples in time 0 , 1hour, 2hours, 3 hours and 4 hours. I
will name each of the replicates as 0hour-1, 0hour-2, 0hour-3,etc.
I will first compare expression between 0hour and 1hour.
I will use cuffmerge to merge 0hour-1, 0hour-2, 0hour-3,
1hour-1,1hour-2.1hour-3 to generate one cuffmerge file.
Then I will run cuffdiff using the merged file, include two groups, group 1
is 0 hour (add 0hour 1-3 in group 1) and group 2 is 1hour (add 1hour1-3 in
Does this sound reasonable?
Thank you very much,
Bauer Lab, MCBD
Simon Hall: 313-317
212 S. Hawthorne Dr.
Bloomington, IN 47405
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: