Dear Genome Browser team, I would like to ask for your help regarding the Xenopus genome assembly version that is available on the UCSC Genome Browser, and how it corresponds to Ensembl versions. From the README file in the download directory for the Xenopus genome, I understand that the assembly version that was used is JGI v4.1, released in August 2005. From the Ensembl website, I gathered that this same version was used in most of the latest Ensembl releases (prior to release 62). However, the two fasta files (the one downloaded from the UCSC and the one downloaded from Ensembl) are not the same: the one present in Ensembl has 19,501 contigs, and the one in UCSC has 19,759 contigs; moreover, the sequences are not identical, even for those contigs found in both files.
Could you please help me solve out this issue ? I also noticed that Ensembl annotations are available for download from the UCSC Tables; do these annotations correspond to the assembly version that is available for download on the UCSC website ? Thank you very much for your help ! Best wishes, Anamaria -- Anamaria Necsulea Postdoctoral fellow Center for Integrative Genomics Genopode University of Lausanne CH-1015 Lausanne Switzerland Telephone: ++41 21 692 3962 Fax: ++41 21 692 3965 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
