Thanks Wenwu, that is really useful to know. Best regards,
Andrew -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Wenwu Cui Sent: 02 September 2010 17:32 To: [email protected] Cc: Andrew Craig; genome Subject: Re: [Genome] hg19 fosmid end pairs WI2/G248 clone placements can be found at: ftp://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/mapview/clone/NCBI_clone/WI2_clone.md.gz Wenwu Cui Sr. Bioinformatics Scientist NEXTBIO Cupertino, CA 95014 On Sep 2, 2010, at 8:15 AM, Pieter J. de Jong wrote: > Andrew, > > We are working with UCSC to create a .BED file for the fosmids in the NCBI > Clone Nomenclature format and compatible with the hg19 assembly. Hold on for > a few weeks for this to happen. In the mean time, you can find (and > download) all the fosmid end sequences for this library from the NCBI > TraceArchive using the query string: center_project="G248". That will > provide you with 2,298,885 records for fosmid-ends and annotations, > including the references to the paired-end from the same fosmid. > > NCBI TraceArchive: http://www.ncbi.nlm.nih.gov/Traces/trace.cgi? > > > Pieter J. de Jong, Ph.D. > Principal Investigator KOMP-CSD & Director, BACPAC Resources > Children's Hospital Oakland Research Institute > Bruce Lyon Research Building > 747 52nd Street, Oakland, CA 94609 > 510-450-7919 (phone) and -7951 (fax) > http://bacpac.chori.org > > > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Andrew Craig > Sent: Thursday, September 02, 2010 3:35 AM > To: Ann Zweig > Cc: genome > Subject: Re: [Genome] hg19 fosmid end pairs > > Ann and Jen > > Thank you both for the information. > > I was going to ask if you could provide the sequence data, but I take it > from you're post that you probably don't actually have it? Do you happen to > know if the sequence data is publically available anywhere? I can only find > a small number of sequences in NCBI nucleotide and nothing in EMBL. > > The UCSC browser is about the only place I have found where you can get > *any* mapping data for the WIBR-2 fosmid library so I really appreciate you > making the effort to make that data available. If in future versions of the > track you could also include the bacpac style clone id's e.g. WI2-1A1 style, > that would be even better! > > Best regards, > > Andrew > > > -----Original Message----- > From: [email protected] > [mailto:[email protected]] On Behalf Of Ann Zweig > Sent: 01 September 2010 17:50 > To: Andrew Craig > Cc: genome > Subject: Re: [Genome] hg19 fosmid end pairs > > Hello again, Andrew, > > Just a bit more information on this topic. When Jen said we didn't have > plans to > add it in the *near* future, she was correct. However, we do have plans to > add > it at some point. We are waiting for a collaborator to help us generate the > tracks. As soon as that happens, we will make the track available on the > hg19 > browser. > > Regards, > > ---------- > Ann Zweig > UCSC Genome Bioinformatics Group > http://genome.ucsc.edu > > > On 08/31/10 13:29, Jennifer Jackson wrote: >> Hello Andrew, >> >> We are very sorry, but there are no plans to add this dataset in the >> near future. But, please feel free to check back in with our the mailing >> list support team for an update later on. >> >> Warm regards, >> >> Jen >> UCSC Genome Browser Support >> >> On 8/31/10 7:13 AM, Andrew Craig wrote: >>> Dear List, >>> >>> The hg19 annotation database has a set of fosmid end pairs, i.e. > http://hgdownload.cse.ucsc.edu/goldenPath/hg18/database/fosEndPairs.txt.gz >>> >>> I'm looking for fosmid end pair data for the hg19 assembly but there > does not seem to be an equivalent file in > http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/ >>> >>> Does this data set not exist for hg19, or is there somewhere else I > should be looking? >>> >>> Best regards, >>> >>> Andrew Craig >>> >>> > ---------------------------------------------------------------------------- > ------------------------------------------------------------- >>> This email is confidential and privileged. 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