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. If you are not the intended >> recipient please accept our apologies; please do not disclose, copy, or >> distribute information in this email nor take any action in reliance on >> its contents: to do so is strictly prohibited and may be unlawful. >> Please inform us that this message has gone astray before deleting it. >> Thank you for your co-operation. >> ---------------------------------------------------------------------------- ------------------------------------------------------------- >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome ---------------------------------------------------------------------------- ------------------------------------------------------------- This email is confidential and privileged. If you are not the intended recipient please accept our apologies; please do not disclose, copy, or distribute information in this email nor take any action in reliance on its contents: to do so is strictly prohibited and may be unlawful. Please inform us that this message has gone astray before deleting it. Thank you for your co-operation. ---------------------------------------------------------------------------- ------------------------------------------------------------- _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
