Hello Chirag, The Conservation track in the human database has this release of zebrafish included, although any genome sequence that is in zebrafish and not in human would be not included (all data is anchored to the human genome). Galaxy has a tool that will "re-order" a MAF based on the genomes included. You may find this helpful. They have a help group that can offered detailed instructions. The idea would be to send over the MAF data of interest from the Table browser and during the output phase of the query, check the "Galaxy" button. The entire dataset is probably too large send as one piece. Try sending regions of interest only or breaking the data up into smaller genome sections (perhaps only those containing zebrafish alignment data, one of the filter options in the Table browser).
If you were to have access to more net/chain data, or other species in a Conservation track (MAF) alignment, which would be the most important to you (ranking in order of importance)? There are no definitive plans to expand the dataset, but user feedback is always important to us when we prioritize projects, so your input would be very welcomed. Thanks, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 2/15/10 2:49 PM, [email protected] wrote: > Dear UCSC, > > Though the official release of Zv8 is out now,it would be great if > have more chain alignments and net chain alignment, though they are in > test browser, it would be good to have in .axt format in main browser. > > I would like to know when will the MSA of Zv8 with other organism and > the phastcons track will be out on the browser. It would be great for > many of us, mostly working on zebrafish, if it will be out soon on the > browser. > > Thank you for your help in advance !! > > regards > Chirag Nepal > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
