Thanks for your detailed reply! I think I'll stick with the much simpler mafSubset to get going and can still improve or update it later.
Concerning the alignments: For us, one single intra-fish alignment would be useful. As zebrafish is the most common fish model, it could be the base. People could then still reorder/subset the zebrafish mafs if they need it on a different fish base genome. Ensembl has avian and fish-alignments ( http://ensembl.blogspot.com/2010/03/new-avian-and-new-fish-mutliple.html) but these are difficult to get imported into the browser and they use a different pipeline. Apart from the fish, with human and mouse as in your older version of this alignment, I don't think there are other assemblies that need to be added, at least not for our application. thanks again Max On Tue, Apr 20, 2010 at 7:10 AM, Jennifer Jackson <[email protected]> wrote: > 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
