On Mon, 21 Nov 2011, Brooke Rhead wrote: > You could turn that into a BED format file > (http://genome.ucsc.edu/FAQ/FAQformat.html#format1) by changing those lines > into: > > chr1 55549 55550 > chr1 82570 82571 > chr1 88168 88169
Fantastic. I had no idea how close I was. I had made a file almost exactly like that except that I had repeated the value from column 2 in column 3 instead of adding one to it. Once I added one to it, it worked. I didn't realize that the "feature" defined by chromStart and chromEnd would not exist unless chromEnd were greater than chromStart (and not merely equal to it), but looking again at the documentation for the BED format, I think it's pretty clear. The result of my mistake was that every marker was deleted. One more question if you have a minute: 54 of my markers were listed as "Deleted in new" in the "unMapped" file. What's the best way of finding good positions for those SNPs? Any idea why they are missing? I found this file... b135_SNPChrPosOnRef_37_3.bcp ...but rs numbers for only 11 of the 54 markers are listed in that file. Thanks so much for your help. Mike -- Michael B. Miller, Ph.D. Minnesota Center for Twin and Family Research Department of Psychology University of Minnesota _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
