This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Annotation File For Mm10 For Methylkit/Rrbs

In the user guid for MethlyKit it gives brief instructions on using an annotated BED file to give differential methylation in promoter/intron/exon regions globally.

gene.obj<- read.transcript.features("subset.refseq.hg18.bed.txt") annotate.WithGenicParts(myDiff25p,gene.obj)

MethylKit comes with the "subset...." file, but this is not a complete annotation and furthermore is not the genome I need.

It says one needs to use Bioconductor/Genomic Features to obtain a complete annotation.

I'm looking for an annotated mm10 BED file, but the computer cluster I work on does not support GenomicFeatures(but is in the process of obtaining the software to do so).

Does anyone know where I can obtain an annotated mm10 BED file without using Genomic Features/Bioconductor?

Thanks!

annotation bioconductor
• 7,271 views • link
written by simonconti • simonconti

1 answer

yes: Recap: select mm10 version from ucsc tables -->genes and genes prediction tracks -->refseq genes --> output format -->bed -->output file: mm10.refseq.genes.bed

• 0 views • link
written by Rm Rm

Log in to answer this question.

More posts like this