Best way to get updated annotation for BACs
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Daniel Brewer ★ 1.9k
@daniel-brewer-1791
Last seen 10.2 years ago
Hello, I am dealing with a BACs microarray, but the annotation I have is from an old version of the human genome. Could anyone suggest some ways of updating the information to hg19? I would initially like the positional information, but also want gene(s) the BAC covers and whether the BAC covers the whole gene or whether it is at the front or back. For each BAC I have a clone name e.g. RP11-172L12 and a ChoriID N0172L12. Many thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis Email: daniel.brewer at icr.ac.uk ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}
Microarray Annotation Cancer BAC Microarray Annotation Cancer BAC • 1.5k views
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@sean-davis-490
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On Wed, Nov 3, 2010 at 7:12 AM, Daniel Brewer <daniel.brewer@icr.ac.uk>wrote: > Hello, > > I am dealing with a BACs microarray, but the annotation I have is from > an old version of the human genome. Could anyone suggest some ways of > updating the information to hg19? I would initially like the positional > information, but also want gene(s) the BAC covers and whether the BAC > covers the whole gene or whether it is at the front or back. For each > BAC I have a clone name e.g. RP11-172L12 and a ChoriID N0172L12. > > Hi, Daniel. Check out the bacEndPairs track at UCSC. The name column will contain the clone name. You could use the table browser to get the data that you want or just download the whole table. A workflow of rtracklayer track downloads into IRanges objects of one type or another for genes and bac-ends would allow you to get the overlap of bac-ends with genes; I don't have details at hand, but the data sources are easily available. Sean [[alternative HTML version deleted]]
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That's great, many thanks for that. The only problem I am having is that some of the clones do not come up in the bacEndPairs table, for example RP11-363L4 or CTD-2001A18. When I search for these in Ensembl they sometimes are there as a sequence, but sometimes not. Any ideas? The non-matching clones are about two thirds of the set. Many thanks Dan On 03/11/2010 12:02 PM, Sean Davis wrote: > > > On Wed, Nov 3, 2010 at 7:12 AM, Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> <mailto:daniel.brewer at="" icr.ac.uk="">> wrote: > > Hello, > > I am dealing with a BACs microarray, but the annotation I have is from > an old version of the human genome. Could anyone suggest some ways of > updating the information to hg19? I would initially like the positional > information, but also want gene(s) the BAC covers and whether the BAC > covers the whole gene or whether it is at the front or back. For each > BAC I have a clone name e.g. RP11-172L12 and a ChoriID N0172L12. > > > Hi, Daniel. > > Check out the bacEndPairs track at UCSC. The name column will contain > the clone name. You could use the table browser to get the data that > you want or just download the whole table. A workflow of rtracklayer > track downloads into IRanges objects of one type or another for genes > and bac-ends would allow you to get the overlap of bac-ends with genes; > I don't have details at hand, but the data sources are easily available. > > Sean -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis MUCRC 15 Cotswold Road Sutton, Surrey SM2 5NG United Kingdom Tel: +44 (0) 20 8722 4109 ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}
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On Wed, Nov 3, 2010 at 9:49 AM, Daniel Brewer <daniel.brewer@icr.ac.uk>wrote: > That's great, many thanks for that. The only problem I am having is > that some of the clones do not come up in the bacEndPairs table, for > example RP11-363L4 or CTD-2001A18. When I search for these in Ensembl > they sometimes are there as a sequence, but sometimes not. Any ideas? > The non-matching clones are about two thirds of the set. > > That figures.... Do you have the original design file with genomic locations? If so, use the UCSC liftover tool to go from the old genome to the genome of your choice. Have the arrays been used in a published experiment? If so, the design file may be available via NCBI GEO or ArrayExpress. Sean > Many thanks > > Dan > > On 03/11/2010 12:02 PM, Sean Davis wrote: > > > > > > On Wed, Nov 3, 2010 at 7:12 AM, Daniel Brewer <daniel.brewer@icr.ac.uk> > <mailto:daniel.brewer@icr.ac.uk>> wrote: > > > > Hello, > > > > I am dealing with a BACs microarray, but the annotation I have is > from > > an old version of the human genome. Could anyone suggest some ways > of > > updating the information to hg19? I would initially like the > positional > > information, but also want gene(s) the BAC covers and whether the BAC > > covers the whole gene or whether it is at the front or back. For > each > > BAC I have a clone name e.g. RP11-172L12 and a ChoriID N0172L12. > > > > > > Hi, Daniel. > > > > Check out the bacEndPairs track at UCSC. The name column will contain > > the clone name. You could use the table browser to get the data that > > you want or just download the whole table. A workflow of rtracklayer > > track downloads into IRanges objects of one type or another for genes > > and bac-ends would allow you to get the overlap of bac-ends with genes; > > I don't have details at hand, but the data sources are easily available. > > > > Sean > > -- > ************************************************************** > > Daniel Brewer, Ph.D. > > Institute of Cancer Research > Molecular Carcinogenesis > MUCRC > 15 Cotswold Road > Sutton, Surrey SM2 5NG > United Kingdom > > Tel: +44 (0) 20 8722 4109 > > ************************************************************** > > The Institute of Cancer Research: Royal Cancer Hospital, a charitable > Company Limited by Guarantee, Registered in England under Company No. 534147 > with its Registered Office at 123 Old Brompton Road, London SW7 3RP. > > This e-mail message is confidential and for use by the...{{dropped:13}}
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On 03/11/2010 5:11 PM, Sean Davis wrote: > Do you have the original design file with genomic locations? If so, use > the UCSC liftover tool to go from the old genome to the genome of your > choice. Have the arrays been used in a published experiment? If so, > the design file may be available via NCBI GEO or ArrayExpress. > > Sean Yes I do have the original design files, so the liftover tool should work. Great. Many thanks Dan -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis MUCRC 15 Cotswold Road Sutton, Surrey SM2 5NG United Kingdom Tel: +44 (0) 20 8722 4109 ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}
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Hello, Sorry to come back onto this, but I can't get Lift Genome Annotations (http://genome.ucsc.edu/cgi-bin/hgLiftOver) to work whatever I do. Has anyone else had any success with this tool? I always get "#Deleted in new" for all the Clone's positions. In fact, even if I try a test like "Chr1:100000-100001", I get the same error. Apologies for needing my hand held on this one. Dan On 03/11/2010 5:11 PM, Sean Davis wrote: > > > On Wed, Nov 3, 2010 at 9:49 AM, Daniel Brewer <daniel.brewer at="" icr.ac.uk=""> <mailto:daniel.brewer at="" icr.ac.uk="">> wrote: > > That's great, many thanks for that. The only problem I am having is > that some of the clones do not come up in the bacEndPairs table, for > example RP11-363L4 or CTD-2001A18. When I search for these in Ensembl > they sometimes are there as a sequence, but sometimes not. Any ideas? > The non-matching clones are about two thirds of the set. > > > That figures.... > > Do you have the original design file with genomic locations? If so, use > the UCSC liftover tool to go from the old genome to the genome of your > choice. Have the arrays been used in a published experiment? If so, > the design file may be available via NCBI GEO or ArrayExpress. > > Sean > > > > Many thanks > > Dan > > On 03/11/2010 12:02 PM, Sean Davis wrote: > > > > > > On Wed, Nov 3, 2010 at 7:12 AM, Daniel Brewer > <daniel.brewer at="" icr.ac.uk="" <mailto:daniel.brewer="" at="" icr.ac.uk=""> > > <mailto:daniel.brewer at="" icr.ac.uk="" <mailto:daniel.brewer="" at="" icr.ac.uk="">>> > wrote: > > > > Hello, > > > > I am dealing with a BACs microarray, but the annotation I have > is from > > an old version of the human genome. Could anyone suggest some > ways of > > updating the information to hg19? I would initially like the > positional > > information, but also want gene(s) the BAC covers and whether > the BAC > > covers the whole gene or whether it is at the front or back. > For each > > BAC I have a clone name e.g. RP11-172L12 and a ChoriID N0172L12. > > > > > > Hi, Daniel. > > > > Check out the bacEndPairs track at UCSC. The name column will contain > > the clone name. You could use the table browser to get the data that > > you want or just download the whole table. A workflow of rtracklayer > > track downloads into IRanges objects of one type or another for genes > > and bac-ends would allow you to get the overlap of bac-ends with > genes; > > I don't have details at hand, but the data sources are easily > available. > > > > Sean > > -- > ************************************************************** > > Daniel Brewer, Ph.D. > > Institute of Cancer Research > Molecular Carcinogenesis > MUCRC > 15 Cotswold Road > Sutton, Surrey SM2 5NG > United Kingdom > > Tel: +44 (0) 20 8722 4109 > > ************************************************************** > > The Institute of Cancer Research: Royal Cancer Hospital, a > charitable Company Limited by Guarantee, Registered in England under > Company No. 534147 with its Registered Office at 123 Old Brompton > Road, London SW7 3RP. > > This e-mail message is confidential and for use by the a...{{dropped:2}} > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch <mailto:bioconductor at="" stat.math.ethz.ch=""> > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > > -- ************************************************************** Daniel Brewer, Ph.D. Institute of Cancer Research Molecular Carcinogenesis MUCRC 15 Cotswold Road Sutton, Surrey SM2 5NG United Kingdom Tel: +44 (0) 20 8722 4109 ************************************************************** The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the a...{{dropped:2}}
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On Thu, Nov 4, 2010 at 9:46 AM, Daniel Brewer <daniel.brewer@icr.ac.uk>wrote: > Hello, > > Sorry to come back onto this, but I can't get Lift Genome Annotations > (http://genome.ucsc.edu/cgi-bin/hgLiftOver) to work whatever I do. Has > anyone else had any success with this tool? I always get "#Deleted in > new" for all the Clone's positions. In fact, even if I try a test like > "Chr1:100000-100001", I get the same error. Apologies for needing my > hand held on this one. > > Hi, Dan. The chromosome names need to match UCSC. I see a capital "C" above. This will not match, so UCSC will not recognize the chromosome name. Sean > Dan > > On 03/11/2010 5:11 PM, Sean Davis wrote: > > > > > > On Wed, Nov 3, 2010 at 9:49 AM, Daniel Brewer <daniel.brewer@icr.ac.uk> > <mailto:daniel.brewer@icr.ac.uk>> wrote: > > > > That's great, many thanks for that. The only problem I am having is > > that some of the clones do not come up in the bacEndPairs table, for > > example RP11-363L4 or CTD-2001A18. When I search for these in > Ensembl > > they sometimes are there as a sequence, but sometimes not. Any ideas? > > The non-matching clones are about two thirds of the set. > > > > > > That figures.... > > > > Do you have the original design file with genomic locations? If so, use > > the UCSC liftover tool to go from the old genome to the genome of your > > choice. Have the arrays been used in a published experiment? If so, > > the design file may be available via NCBI GEO or ArrayExpress. > > > > Sean > > > > > > > > Many thanks > > > > Dan > > > > On 03/11/2010 12:02 PM, Sean Davis wrote: > > > > > > > > > On Wed, Nov 3, 2010 at 7:12 AM, Daniel Brewer > > <daniel.brewer@icr.ac.uk <mailto:daniel.brewer@icr.ac.uk=""> > > > <mailto:daniel.brewer@icr.ac.uk <mailto:daniel.brewer@icr.ac.uk="">>> > > wrote: > > > > > > Hello, > > > > > > I am dealing with a BACs microarray, but the annotation I have > > is from > > > an old version of the human genome. Could anyone suggest some > > ways of > > > updating the information to hg19? I would initially like the > > positional > > > information, but also want gene(s) the BAC covers and whether > > the BAC > > > covers the whole gene or whether it is at the front or back. > > For each > > > BAC I have a clone name e.g. RP11-172L12 and a ChoriID > N0172L12. > > > > > > > > > Hi, Daniel. > > > > > > Check out the bacEndPairs track at UCSC. The name column will > contain > > > the clone name. You could use the table browser to get the data > that > > > you want or just download the whole table. A workflow of > rtracklayer > > > track downloads into IRanges objects of one type or another for > genes > > > and bac-ends would allow you to get the overlap of bac-ends with > > genes; > > > I don't have details at hand, but the data sources are easily > > available. > > > > > > Sean > > > > -- > > ************************************************************** > > > > Daniel Brewer, Ph.D. > > > > Institute of Cancer Research > > Molecular Carcinogenesis > > MUCRC > > 15 Cotswold Road > > Sutton, Surrey SM2 5NG > > United Kingdom > > > > Tel: +44 (0) 20 8722 4109 > > > > ************************************************************** > > > > The Institute of Cancer Research: Royal Cancer Hospital, a > > charitable Company Limited by Guarantee, Registered in England under > > Company No. 534147 with its Registered Office at 123 Old Brompton > > Road, London SW7 3RP. > > > > This e-mail message is confidential and for use by the > a...{{dropped:2}} > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch <mailto:> Bioconductor@stat.math.ethz.ch> > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > > > -- > ************************************************************** > > Daniel Brewer, Ph.D. > > Institute of Cancer Research > Molecular Carcinogenesis > MUCRC > 15 Cotswold Road > Sutton, Surrey SM2 5NG > United Kingdom > > Tel: +44 (0) 20 8722 4109 > > ************************************************************** > > The Institute of Cancer Research: Royal Cancer Hospital, a charitable > Company Limited by Guarantee, Registered in England under Company No. 534147 > with its Registered Office at 123 Old Brompton Road, London SW7 3RP. > > This e-mail message is confidential and for use by the...{{dropped:13}}
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