Good Afternoon Tam: Upon further inspection here, this appears to be an error I made here during construction of this AGP file. These entries appear to indicate gaps where no gap actually exists. Their length of -1 as you have noticed makes them nonsense. They are not in the gap tables and do not show up in the genome browser. They are extra garbage in this one agp file. You can filter them out with this awk command:
$ awk '$3-$2 > 0' chrY_random.agp --Hiram Sneddon, Tam (NIH/NLM/NCBI) [E] wrote: > 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
