retrieveGenomicFeatureAnnotation.R file supplied with Ringo
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Paul Geeleher ★ 1.3k
@paul-geeleher-2679
Last seen 8.1 years ago
Hi, I've been following the instructions in the Ringo manual and using this file to associate my Chip Enriched regions with genomic features. Thing is it seems that in retrieveGenomicFeatureAnnotation.R biomaRt is querying the HG19 genome build. I haven't been able to find a way of changing this to HG18, having searched the web I don't think it's possible? If there is no way of explicitly specifying the genome build maybe it would be worth noting somewhere in the file or documentation that biomaRt is using HG19? Just that I guess the fast majority of people will be using microarrays based on HG18? As an alternative I think I'm just going to try reading gene locations from a BED file on the UCSC site. Sincerely, Paul -- Paul Geeleher School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com
biomaRt Ringo biomaRt Ringo • 729 views
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@joern-toedling-3465
Last seen 8.1 years ago
Hello, by default, the biomaRt functions listed in the script query the current version of Ensembl, and the genome assemblies thus are those used in the current Ensembl release. However, it is possible to connect to an archived version of Ensembl which may contain a previous version of your respective genome build. For a table of available archived marts, you can use > listMarts(archive=TRUE) and then connect to one of those by specifying for example > ensembl <- useMart("ensembl_mart_43", dataset="hsapiens_gene_ensembl", archive=TRUE) and then you should be able to use the rest of the script as with the current one. There might be minor problems because sometimes attributes get renamed between Ensembl releases, but usually one can resolve these by looking at > listAttributes(ensembl) For checking assembly versions in Ensembl releases, however, I think that you first need to consult the Ensembl archive pages before picking one. I am not aware of a more automated way to select the mart based on the desired genome assembly. Regards, Joern On Thu, 4 Mar 2010 12:10:25 +0000, Paul Geeleher wrote > Hi, > > I've been following the instructions in the Ringo manual and using > this file to associate my Chip Enriched regions with genomic > features. Thing is it seems that in > retrieveGenomicFeatureAnnotation.R biomaRt is querying the HG19 > genome build. I haven't been able to find a way of changing this to > HG18, having searched the web I don't think it's possible? If there > is no way of explicitly specifying the genome build maybe it would > be worth noting somewhere in the file or documentation that biomaRt > is using HG19? Just that I guess the fast majority of people will be > using microarrays based on HG18? > > As an alternative I think I'm just going to try reading gene > locations from a BED file on the UCSC site. > > Sincerely, > > Paul
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Ah that's exactly what I was looking for, thank you for you're help. For the record: ensembl <- useMart("ensembl_mart_51", dataset="hsapiens_gene_ensembl", archive=TRUE) will get you the hg18(NCBI36) genome build. On Thu, Mar 4, 2010 at 1:15 PM, Joern Toedling <joern.toedling at="" curie.fr=""> wrote: > Hello, > > by default, the biomaRt functions listed in the script query the current > version of Ensembl, and the genome assemblies thus are those used in the > current Ensembl release. > > However, it is possible to connect to an archived version of Ensembl which may > contain a previous version of your respective genome build. > For a table of available archived marts, you can use > >> listMarts(archive=TRUE) > > and then connect to one of those by specifying for example > >> ensembl <- useMart("ensembl_mart_43", dataset="hsapiens_gene_ensembl", > archive=TRUE) > > and then you should be able to use the rest of the script as with the current > one. There might be minor problems because sometimes attributes get renamed > between Ensembl releases, but usually one can resolve these by looking at > >> listAttributes(ensembl) > > For checking assembly versions in Ensembl releases, however, I think that you > first need to consult the Ensembl archive pages before picking one. I am not > aware of a more automated way to select the mart based on the desired genome > assembly. > > Regards, > Joern > > On Thu, 4 Mar 2010 12:10:25 +0000, Paul Geeleher wrote >> Hi, >> >> I've been following the instructions in the Ringo manual and using >> this file to associate my Chip Enriched regions with genomic >> features. Thing is it seems that in >> retrieveGenomicFeatureAnnotation.R biomaRt is querying the HG19 >> genome build. I haven't been able to find a way of changing this to >> HG18, having searched the web I don't think it's possible? If there >> is no way of explicitly specifying the genome build maybe it would >> be worth noting somewhere in the file or documentation that biomaRt >> is using HG19? Just that I guess the fast majority of people will be >> using microarrays based on HG18? >> >> As an alternative I think I'm just going to try reading gene >> locations from a BED file on the UCSC site. >> >> Sincerely, >> >> Paul > -- Paul Geeleher School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland -- www.bioinformaticstutorials.com
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