Hello Max, The 2nd options would be better scientifically, since just limiting the MAF lines does not recompute the associated calculations (phyloP, phastCons). But creating the Conservation MAF can be tricky. Given your experience with the browser, this may be less of a concern than normally.
If the associated Conservation tracks are not important for you, and a MAF is enough, this makes option 1 simpler, as you describe. One issue that can come up with using an alternate base reference genome is that the assemblies brought in would not necessarily have full representation (some regions will be unique to them, or at least not represented in the alternate reference genome, and so would be excluded). There has been some discussion about creating a Conservation track for danRer6 to include the fish and perhaps a few other selected assemblies. We have been asking interested users which assemblies they would find most useful to include. Would you be like to tell us your "wish list" of assemblies for a danRer6 Conservation track? There is no guarantee (of course) about including these, but the feedback is very helpful and can influence the final decision. If an update is available in the next few days about a danRer Conservation track, I can share that with you (and the other interested users) by posting an update to your question to the mailing list. Great question, I hope the reply is little bit helpful, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/18/10 5:03 AM, Maximilian Haussler wrote: > Hi Gurus, > > I am searching for a fish (at least zebrafish/medaka/stickleback) multiple > alignment with zebrafish as the base. There is none on any zebrafish > assembly but I can see the right chains on danRer6. > I've also found an alignment of danRer5/oryLat2/gasAcu1/tetNig1/fr1 on > oryLat2 as the base. > > Now, I could use mafOrder on the maf files from oryLat2 and remove fugu and > tetraodon with mafSubset to get what I need. An alternative would be to > create the maf file based on the net files from danRer5 with axtToMaf. > > I have a feeling that the 2nd option will give better results but I am not > sure. What do you think? > > thanks! > cheers > Max > -- > Maximilian Haussler > Tel: +447542993736 +447574054746 > http://www.ls.manchester.ac.uk/people/profile/index.asp?id=4774 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
