Dear all,

I've processed the resequenced samples
GK3R7r_G1
GK3R5r_U2
and included them into the previous group of samples
for a MDS plot.

As you can see,
GK3R7r_G1
clusters with the G group
while 
GK3R5r_U2 is distinct from both the G and U group
(note however that GK3R5r_U2 has only 1663880 reads,
which is ~50% of all other samples).


You can also see again that the previous
GK3R7_G1
clusters with the U group
and
GK3R5_U2
clusters with the G group.

From this, I'd conclude that
GK3R5_U2 is very likely GK3R7r_G1.

BW,
Martin





Dear Vasso,

please verify that the files have the following sizes (in Bytes):
5456621 cuffdiff_Gcondition_vs_U/gene_exp.diff.xlsx
5574208 cuffdiff_G_vs_U_delG1+U2/gene_exp.diff.xlsx
5642160 cuffdiff_G_vs_U_G1swapU2/gene_exp.diff.xlsx
5456621 cuffdiff_G_vs_U/gene_exp.diff.xlsx	     
5477118 cuffdiff_Tcondition_vs_U/gene_exp.diff.xlsx
5571612 cuffdiff_T_vs_U_delG1+U2/gene_exp.diff.xlsx
5592037 cuffdiff_T_vs_U_G1swapU2/gene_exp.diff.xlsx
5477118 cuffdiff_T_vs_U/gene_exp.diff.xlsx	     

BW,
Martin


I meant the excel files of T vs U, T vs U swapG1U2, T vs U delG1U2 and the respective G series are the same (see the attached files that I downloaded as an example). I am not sure if I am doing something wrong.

#@
Dear Vasso,


the reports as discussed with Pantelis are:
contrast                 URL
cuffdiff_G_vs_U          http://genomics-lab.fleming.gr/fleming/GKlab/run296/cuffdiff_G_vs_U/cufflinks_report.html	  
cuffdiff_T_vs_U          http://genomics-lab.fleming.gr/fleming/GKlab/run296/cuffdiff_T_vs_U/cufflinks_report.html	  
cuffdiff_T_vs_U_G1swapU2 http://genomics-lab.fleming.gr/fleming/GKlab/run296/cuffdiff_T_vs_U_G1swapU2/cufflinks_report.html
cuffdiff_G_vs_U_G1swapU2 http://genomics-lab.fleming.gr/fleming/GKlab/run296/cuffdiff_G_vs_U_G1swapU2/cufflinks_report.html
cuffdiff_T_vs_U_delG1+U2 http://genomics-lab.fleming.gr/fleming/GKlab/run296/cuffdiff_T_vs_U_delG1+U2/cufflinks_report.html
cuffdiff_G_vs_U_delG1+U2 http://genomics-lab.fleming.gr/fleming/GKlab/run296/cuffdiff_G_vs_U_delG1+U2/cufflinks_report.html


Best wishes,
Martin




Dear Pantelis,


at
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/GKlab/run296/hub.txt
you find tracks for GKlabs run296
normalized to the smallest sample GK3R6-U3.

sample		n_reads
GK3R1-T1	4644186 
GK3R2-T2	4291953 
GK3R3-T3	3953114 
GK3R4-U1	3970351 
GK3R5-U2	5103078 
GK3R6-U3	3767739 
GK3R7-G1	4941242 
GK3R8-G2	5007997 
GK3R9-G3	10300128

The cufflinks results are:

http://genomics-lab.fleming.gr/fleming/GKlab/run296/cuffdiff_T_vs_U/T_vs_U_isoforms_MDSplot.png
http://genomics-lab.fleming.gr/fleming/GKlab/run296/cuffdiff_T_vs_U/T_vs_U_known_genes_alpha0.002_with_replicates.png
http://genomics-lab.fleming.gr/fleming/GKlab/run296/cuffdiff_T_vs_U/isoform_exp.diff.xlsx


http://genomics-lab.fleming.gr/fleming/GKlab/run296/cuffdiff_G_vs_U/G_vs_U_isoforms_MDSplot.png
http://genomics-lab.fleming.gr/fleming/GKlab/run296/cuffdiff_G_vs_U/G_vs_U_known_genes_alpha0.05_with_replicates.png
http://genomics-lab.fleming.gr/fleming/GKlab/run296/cuffdiff_G_vs_U/isoform_exp.diff.xlsx


'Vanilla' metaseqR results are at:
http://genomics-lab.fleming.gr/fleming/GKlab/run296/metaseqr_T_vs_U/index.html
http://genomics-lab.fleming.gr/fleming/GKlab/run296/metaseqr_G_vs_U/index.html

Processing steps are at:
http://genomics-lab.fleming.gr/fleming/GKlab/run296/README-processing.txt

BW,
Martin