Dear Panagiotis,

I've made the 2 DE analysis. Results are at

http://genomics-lab.fleming.gr/fleming/GKlab/Roumelioti/run139
in the dirs:
cuffdiff_GKR13-wt1early_vs_GKR2-DARE1early
cuffdiff_GKR7-wt1late_vs_GKR8-DARE1late

BW,
Martin


@@
Panagiotis Chouvardas
Feb 9,2015

to me 
The contrast groups are DAREearly VS WTearly and DARElate VS WTlate. I think the 1st samples of each group are those missing, so it can not be done at the moment.
If it is any kind of trouble, there is no problem running the differential expression analysis myself. 

Best,
P.

@@ 09022015
Dear Panagiotis,

of the 6 Proton runs, 4 have finished my analysis.
You can find these 4 at
http://genomics-lab.fleming.gr/fleming/GKlab/Roumelioti/
in the dirs
run130
run132
run134
run135

In each dir, the file
samples.txt
describes the identity of each sample and basic stats (#reads ...).

In each dir, there is a dir called
tophat_XXX
for each barcode XXX.

In these dirs, the file
sort_uniq.bam
is the final file with all reads and alignments to mm9.
If you want to use Cufflinks, you shound add a header to these
with
samtools reheader ...
.

The other 2 runs should finish tomorrow evening.
Let me know is you need any help.

Best wishes,
Martin