Dear Vangelis

at
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/GKlab/run339/hub.txt
you will find tracks for the samples in run339, (normalized to the 2nd smallest library, GK3R105_TR1 with 3588162 reads.
The smallest library, GK3R99_TU1 is kept without sampling):

sample      n_reads
GK3R99_TU1  616257
GK3R100_TU2 4473940
GK3R101_TU3 8455855
GK3R102_TH1 4327304
GK3R103_TH2 4349738
GK3R104_TH3 4185805
GK3R105_TR1 3588162
GK3R106_TR2 4237539
GK3R107_TR3 5324689
GK3R108_WU1 4111069
GK3R109_WU2 4468556
GK3R110_WU3 5867941

At http://genomics-lab.fleming.gr/fleming/GKlab/run339/metaseqr_quantseq_run339/index.html 
you will find the metaseqR [1] differential gene expression analysis using
the contrasts
"WU_vs_TU",	"WU_vs_TH",		"WU_vs_TR",	"TU_vs_TH",	"TU_vs_TR",	"TH_vs_TR"
(note the used naming convention: in A_vs_B, A is always the reference).

The origin of the 8279911 reads that were assigned to barcode 001 can be assessed at
http://genomics-lab.fleming.gr/fleming/GKlab/run339/metaseqr_quantseq_run339_with_UNK/index.html
These reads show no similarity to the other samples, except a very low correlation of 0.21 with TU1.

Please forward this.
BW,
Martin


[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.