Hi Shamsher, Yes, can you send me your list and the URL to the Illumina file?
- Greg On 3/17/11 12:06 PM, shamsher jagat wrote: > HI Greg, > > I sent you the following message and am not sure if you received it. > Please advice me whenever you get a chance. > > Shamsher > > ---------- Forwarded message ---------- > From: *shamsher jagat* <[email protected] <mailto:[email protected]>> > Date: Wed, Mar 16, 2011 at 5:57 PM > Subject: Re: [Genome] getting genomic coordinates > To: Greg Roe <[email protected] <mailto:[email protected]>> > > > Thanks Greg, > I have list of accession numbers (e.g AY293855 - Chr no 6 and > start 140618 and stop 140769) with Chr no and start and end. These > particular regions are reported in the publications as active in a > biological process. I have to take these regions and map to > annotation file from illumina (array based) to find out which probes > may be bindning to these particular regions reported in publications > (publications have used different method of identifying the said > location say e.g RTPCR etc). The annotation file is based on hg18 and > specify binding position of each probe in terms of genmoic locations. > If you think best I can send you list I have and point you to URL of > Ilumina annotation file. > Thanks. > Shamsher > On Wed, Mar 16, 2011 at 5:32 PM, Greg Roe <[email protected] > <mailto:[email protected]>> wrote: > > Hi Shamsher, > > Are you trying to do a lift over from, say, hg19 (or some other > assembly) to hg18? (i.e. you have coordinates and IDs from one > assembly and you're trying to find them in another?). What > assembly are you starting with? With a little more information, I > can better answer your question. > > Thanks, > > Greg > > > On 3/16/11 4:24 PM, shamsher jagat wrote: >> >> What I have is Genebank accession Id like AY293855 - Chr no 6 >> and start 140618 and stop 140769 so I want to find out >> corresponding genomic coordinates in Hg18. >> I dont see any option in the Table- like that Am I missing something? >> Thanks >> >> On Wed, Mar 16, 2011 at 3:19 PM, Greg Roe <[email protected] >> <mailto:[email protected]>> wrote: >> >> Hi Shamsher, >> >> It is possible, but it depends on what time of gene >> identifiers you have. You should take a look at our table >> browser: http://genome.ucsc.edu/cgi-bin/hgTables >> >> For example, if you have refSeq IDs, formatted like >> "NM_001139466", you can select the desired assembly, group: >> genes, track: refSeq, and paste your list of IDs in using the >> identifiers: 'paste list' button, and then click 'get >> output', you'll have the info you want for your IDs. >> >> Please let us know if you have any additional questions. >> - >> Greg Roe >> UCSC Genome Bioinformatics Group >> >> >> >> On 3/16/11 1:44 PM, shamsher jagat wrote: >> >> Is it possible to extract genomic coordinates If I have >> gene accession ID >> Chr stat and end position. Any pointer will be helpful. >> >> Thanks. >> _______________________________________________ >> Genome maillist - [email protected] >> <mailto:[email protected]> >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
