Hello Tam, I can confirm what you are seeing in the file. The data comes directly from the source (in this case for mm9, NCBI). They have an agp file specification here: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/agp/
For gap_type = fragment, this seems to be the way coordinates are used. You might try asking NCBI why they format this way if you are curious, otherwise, simply interpret these to be markers that delimitate unmapped contigs on the artificially created random chromosome (which is basically just a string of unordered contigs). We hope this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Tam Sneddon (NIH/NLM/NCBI) [E]" <[email protected]> wrote: > From: "Tam Sneddon (NIH/NLM/NCBI) [E]" <[email protected]> > To: [email protected] > Sent: Tuesday, January 5, 2010 7:40:42 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] mm9 chrY_random.agp > > Hi: > > I am looking at the chrY_random.agp file downloaded from the following > url: > ftp://hgdownload.cse.ucsc.edu/goldenPath/mm9/bigZips/chromAgp.tar.gz > > Why are there 326 lines with object_end less than object_beg? > Thanks, > > Tam > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
