Thanks for the update Jaaved! - Greg
On 11/14/11 8:04 AM, Jaaved Mohammed wrote: > Hi all, > > > > The folk on the Flybase help mailing list were able to answer my questions > regarding the persimilis and willistoni scaffolding naming discrepancies > between the UCSC genome browser and Flybase: > > > > 1. D. persimilis: > > There is a one-to-one relationship between the UCSC "scaffold_" prefixed > headers and the "super_" prefixed headers. For example, scaffold_14 > corresponds to super_14. > > > > 2. D. willistoni: > > The mapping is not so trivial as it is for persimilis. Both UCSC genome > browser and Flybase uses the AAA CAF1 assemblies produced in 2007. However, > 89 scaffolds from the CAF1 assembly for Dwil were later suppressed from the > CAF1 assembly before it was added to GenBank because these 89 scaffolds > mapped to Wolbachia. The scaffold IDs were also changed to avoid confusion > with the previous (original) assembly. Explicitly, it appears that UCSC > genome browser is using the unsuppressed, original willistoni assembly and > Flybase is using the modified assembly. > > > > A mapping between the original AAA version and what exists in > GenBank/FlyBase can be found here: > > ftp://ftp.ncbi.nih.gov/genomes/Drosophila_melanogaster/special_requests/CAF1 > /dwil/dwil_scaffold2GenBank > > > > A full list of problematic scaffolds that were found during the GenBank > submission process (for all 12 Drosophila genomes) can be found here: > > ftp://ftp.ncbi.nih.gov/genomes/Drosophila_melanogaster/special_requests/CAF1 > /foreign_scaffolds_in_caf1.txt > > > > > > > > > > This explanation has been reworded from the response I received on the > Flybase help mailing list. I thank everyone for their generous help with > this ambiguity. Hopefully others who encounter this discrepancy will find a > suitable answer in this thread. > > > > Thanks, > > Jaaved > > > > -- > Jaaved Mohammed, > Ph.D. Student of Computational Biology > Tri-Institutional Training Program in Computational Biology and Medicine > (Cornell University - Ithaca, Weill Cornell Medical College, and Memorial > Sloan-Kettering Cancer Center) _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
