BiomaRt and extracting genomic sequence
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@rs-illingworth-3245
Last seen 8.1 years ago
Hello to the list I have recently started mapping next generation sequencing data to the human genome and would now like to map this to genes and other annotated genomic features. Whilst I have found that I can map and sort genes with the biomaRt package I have completely failed to extract genome sequence using simple chromosome coordinates. I have looked through the documentation for this package and have tried to use the getSequence function but to no avail. The 'seqType' values all seem to relate to gene associated sequences and 'type' has no obvious value for genomic sequence and as such return an error msg. I think there is probably a very straight forward solution which I am missing and I would be very grateful if anyone could help. Thanks for your assistance kind regards Rob Illingworth -- WTCCB Institute of Cell Biology The University of Edinburgh Michel Swann Building Mayfield Road Edinburgh EH9 3JR TEL:+44(0)131 650 8695 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
Sequencing biomaRt Sequencing biomaRt • 2.1k views
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@steffenstatberkeleyedu-2907
Last seen 8.1 years ago
Hi Rob, This is currently not possible using biomaRt in web service mode. However the Ensembl team will probably make this available to us in the near future. If you're using the current release version of biomaRt (1.16.0) then you should be able to get genomic sequences (unfortunately only from Ensembl version 47) by: >mart = useMart("ensembl_mart_47", dataset="hsapiens_gene_ensembl", mysql=TRUE) >seq = getSequence(chromosome = 20, start=20000, end = 20010, mart=mart) > seq chromosome start end sequence 1 20 20000 20010 TGAGGTCTTAC Note that this MySQL mode retrieval of genomic sequences will be replaced by the default web service mode use of biomaRt. Cheers, Steffen > Hello to the list > > I have recently started mapping next generation sequencing data to the > human genome and would now like to map this to genes and other > annotated genomic features. Whilst I have found that I can map and > sort genes with the biomaRt package I have completely failed to > extract genome sequence using simple chromosome coordinates. I have > looked through the documentation for this package and have tried to > use the getSequence function but to no avail. The 'seqType' values all > seem to relate to gene associated sequences and 'type' has no obvious > value for genomic sequence and as such return an error msg. I think > there is probably a very straight forward solution which I am missing > and I would be very grateful if anyone could help. > > Thanks for your assistance > > kind regards > > Rob Illingworth > > -- > WTCCB > Institute of Cell Biology > The University of Edinburgh > Michel Swann Building > Mayfield Road > Edinburgh > EH9 3JR > TEL:+44(0)131 650 8695 > > > > > -- > The University of Edinburgh is a charitable body, registered in > Scotland, with registration number SC005336. > > _______________________________________________ > Bioconductor mailing list > 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 >
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The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.
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