Hello, I have two questions that I would really appreciate your help with answering.
=========== Firstly, =========== I am trying to understand the origin of the "super*" coordinates for the droPer1 and droSec1 genomes available on the UCSC Genome Browser. For example, in the D. sechellia assembly, I see that all the chromosomes are prefixed by "super" on the Genome Browser: http://genome-mirror.bscb.cornell.edu/cgi-bin/hgTracks?hgsid=36382&chromInfo Page=. However, from Flybase.org, the GFF files, or any coordinate for that matter on Flybase, is always prefixed by "scaffold" as can be seen from ftp://flybase.net/genomes/Drosophila_sechellia/current/gff/. Why is this? How were the conversion done from "scaffold" into "super" coordinates? I'm trying to convert the flybase genes reported in the GFF files into a file that I can upload to the browser to see the flybase annotated genes, non-coding RNAs, etc. however this clash of coordinate names is causing much problems. I should note that I looked in all the older revisions of the Flybase GFF files and still I see no "super" prefixed coordinates. I hope I'm not looking at the wrong flybase GFF files. The same observation was made in the droPer1 reference assembly. ============= Secondly, I've noticed that D. willistoni reference assembly is not available on the UCSC Genome Browser. Why is this? I've added this genome to the Cornell mirror using the droWil1.fa file downloaded/available from the UCSC browser. The added genome can be viewed here: http://genome-mirror.bscb.cornell.edu/cgi-bin/hgGateway?hgsid=36387&clade=in sect&org=D.+willistoni&db=0 On a similar note to the first point above, I've observed that the coordinates are prefixed with "scaffold" on the browser, but flybase reports coordinates prefixed with "scf2_": ftp://flybase.net/genomes/Drosophila_willistoni/current/gff/. 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
