Dear Sofia,

using the link, 
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/DKlab/run347/hub.txt
you will find tracks for the 2 QuantSeq runs merged, normalized
to the smallest library (mergedDK3R6-K3) containing 2884541 reads

sample(s)           n_reads
mergedDK3R10b-K23L4 4261384
mergedDK3R11-K2L4   4498530
mergedDK3R12-K3L4   5883918
mergedDK3R1r-C1     3904712
mergedDK3R2r-C2     3808001
mergedDK3R3r-C3     4919353
mergedDK3R4b-K23    3391024
mergedDK3R5-K2      4062319
mergedDK3R6-K3      2884541
mergedDK3R7-C1L4    3835289
mergedDK3R8-C2L4    4237759
mergedDK3R9r-C3L4   3804990

For RIP:
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/DKlab/run392/hub.txt
http://genomics-lab.fleming.gr/cgi-bin/hgTracks?db=mm10&hubUrl=http://genomics-lab.fleming.gr/fleming/DKlab/run392/run402/hub.txt
you will add the 1st 4 tracks (run392) and then the remaining tracks, I just confirmed this is working.



You can also use the last part, eg
http://genomics-lab.fleming.gr/fleming/DKlab/run392/hub.txt
to add the hub manually in 'Track hubs' -> 'My hubs' -> 'URL'

The RIP analysis has proceeded, but due to urgent additional requests by George and Maragita
there is a slight delay and I hope to have an initial result for you tomorrow.

Best wishes,
Martin