Hi Tuuli, others We definitely succeeded in bringing more focus in the paper. I like the rare regulatory variant a lot, but I had to read it many times to be able to understand (most of) it. Perhaps others have also ideas on writing this down more clearly. Other comments in the text of the rebuttal and the paper Best wishes Peter ________________________________ From: geuvadis_rnaseq-bounces(a)lists.crg.es [mailto:geuvadis_rnaseq-bounces@lists.crg.es] On Behalf Of Tuuli Lappalainen Sent: 01 March 2013 10:26 To: geuvadis_rna_analysis(a)lists.crg.es; geuvadis_rnaseq(a)lists.crg.es Subject: [Geuvadis_rnaseq] Geuvadis RNA-seq paper revision Dear all, We have revised the Geuvadis RNA-seq paper for Nature; please find the paper and the response letter enclosed. If you have any comments, please send them by Saturday - apologies for the tight schedule, we are planning to submit this on Monday. Thanks to all of you who helped me with the revisions. As many of you know, the editor adviced us to make the paper more focused on the key messages, and as a consequence we had to drop some of the analyses - fusion transcripts, soft splicing and RNA editing. I hope that those results can be published in some other context later on. To strengthen the analysis of regulatory variants, I did some additional analysis on regulatory variants underlying allele-specific expression signals, but otherwise the changes in the paper are relatively small. I think that we were able to respond to all the comments really well, and hopefully the editor and reviewers agree. best regards, Tuuli -- Tuuli Lappalainen, PhD Department of Genetics, Stanford University School of Medicine , and Department of Genetic Medicine and Development, University of Geneva Email: tuuli.e.lappalainen@gmail.com<mailto:tuuli.e.lappalainen@gmail.com> / tlappala@stanford.edu<mailto:tlappala@stanford.edu> Tel: +1 415 351 9713 Bustamante lab Department of Genetics 300 Pasteur Dr. Lane L301 Stanford, CA 94305-5120 USA