Dear Pantelis

the analysis of the dme RNAseq experiment in run347 has finished.
The samples and the number of reads obtained are:

sample         n_reads
YA3R1-Byn1     1338562
YA3R2-Byn2     3252609
YA3R3-Byn3     1475110
YA3R4-BynRas1  2532928
YA3R5-BynRas2  2123374
YA3R6-BynRas3  2815507

At 
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=dm6&hubUrl=http://genomics-lab.fleming.gr/fleming/external/Apidianakis/run347/hub-dm6.txt
you will find tracks for all samples integrated in our UCSC genome browser mirror.
These tracks are sampled to smallest library (YA3R1-Byn1 with 1338562 reads).

At
http://genomics-lab.fleming.gr/fleming/external/Apidianakis/run347/metaseqr_Apidianakis_run347/index.html
you will find the metaseqR [1] differential gene expression analysis using
the contrast
Byn_vs_Ras, which is
(note the used naming convention: in A_vs_B, A is always the reference).

With best regards,
Martin Reczko

[1] Moulos P and Hatzis P “Systematic integration of RNA-Seq statistical
algorithms for accurate detection of differential gene expression
patterns.” Nucl. Acids Res. (2014)
doi: 10.1093/nar/gku1273
http://nar.oxfordjournals.org/content/early/2014/12/01/nar.gku1273.abstract.