At 
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=hg19&hubUrl=http://genomics-lab.fleming.gr/fleming/EDlab/run423/hg19/hub.txt
(within Fleming: http://filia/cgi-bin/hgTracks?db=hg19&hubUrl=http://filia/fleming/EDlab/run423/hg19/hub.txt )
you will find tracks for all samples integrated in our UCSC genome browser mirror.

Omit wt3 and tg3



Dear Eleni

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

sample         n_reads
ED3R1_K471-wt1 6144646
ED3R2_K513-wt2 7549064
ED3R3_K514-wt3 8172928
ED3R4_K518-wt4 9426622
ED3R5_K473-tg1 7433581
ED3R6_K483-tg2 12090910
ED3R7_K485-tg3 7147062
ED3R8_K517-tg4 8588775

At 
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/EDlab/run423/hub.txt
(within Fleming: http://filia/cgi-bin/hgTracks?db=mm10&hubUrl=http://filia/fleming/EDlab/run423/hub.txt )
you will find tracks for all samples integrated in our UCSC genome browser mirror.
These tracks are sampled to the 2nd smallest library (ED3R7_K485-tg3 with 7147062 reads).
The smallest library, ED3R1_K471-wt1 is kept without sampling.

At
http://genomics-lab.fleming.gr/fleming/EDlab/run423/metaseqr_run423/
(within Fleming: http://filia/fleming/EDlab/run423/metaseqr_run423/ )

you will find the metaseqR [1] differential gene expression analysis using
the contrast
wt_vs_tg, which is
(NOTE the used naming convention: in A_vs_B, A is the reference).
In the "Results" section, there are links to download the diff. expr. results
under "DEG table", "Download the whole result list".

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.



--
Dr. Martin Reczko

Staff research scientist professor level
Institute for Fundamental Biomedical Science
Biomedical Sciences Research Center "Alexander Fleming"
Technical Coordinator - ELIXIR Greece
34 Fleming Street
16672 Vari, Greece
Tel. +30-210-9656310 (ext. 144)
FAX: +30-210-9653934
email: reczko@fleming.gr