[Bioc-devel] rtracklayer::import.bed(genome = Seqinfo)

[Michael Lawrence]

Hi Aditya,

This is probably best asked on the support site. When you post there,
please include your sessionInfo().

Thanks,
Michael

On Tue, Oct 22, 2019 at 9:50 AM Bhagwat, Aditya
<Aditya.Bhagwat using mpi-bn.mpg.de> wrote:
>
> Dear Michael,
>
> Sorry for my incomplete email - the send button got hit too fast. Better this time.
>
> rtracklayer::import.bed mentions the argument "genome" to be either a genome identifier (like 'mm10') or a Seqinfo object.
>
> I notice that the second option does not work on my BED file (in attach).
>
> # This works
> rtracklayer::import.bed('SRF.bed', genome = 'mm10') # this works
>
> # But this doesn't
> seqinfo1<- GenomeInfoDb::seqinfo(BSgenome.Mmusculus.UCSC.mm10::BSgenome.Mmusculus.UCSC.mm10)
> rtracklayer::import.bed('SRF.bed', genome = seqinfo1)
>
> So I am requesting feedback.
> I thought to use this channel
>
> Aditya



-- 
Michael Lawrence
Scientist, Bioinformatics and Computational Biology
Genentech, A Member of the Roche Group
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