Hi Mike, Glad to hear that you are making progress! One thing we would like to clarify is that it is acceptable to have cases where chromStart = chromEnd in BED format. For instance:
chr1 55550 55550 is considered an insertion between base 55550 and 55551. It shows up as a small tick-mark between the two bases in the Genome Browser. With regards to "Deleted in new", please see these previously answered mailing list question: https://lists.soe.ucsc.edu/pipermail/genome/2010-February/021301.html Also, if you are trying to lift specific regions of data to hg18, then you might not be getting mappings because there are some regions of hg19 not in hg18. To see diffs between the two assemblies, you can use these tracks: on hg18 Hg19 Diff: Contigs dropped or changed from NCBI build 36(hg18) to GRCh37(hg19) http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg18&g=hg18ContigDiff on hg19 Hg18 Diff: Contigs new to GRCh37/(hg19), not carried forward from NCBI build 36(hg18) http://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&g=hg19ContigDiff Hope this helps clarify things for you! If you have further questions, please contact the mailing list: [email protected]. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ---------- Forwarded message ---------- From: Mike Miller <[email protected]> Date: Mon, Nov 21, 2011 at 9:27 PM Subject: Re: [Genome] converting from hg18 to hg19 To: Brooke Rhead <[email protected]> Cc: UCSC Genome List <[email protected]> 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
