Annotation File For Mm10 For Methylkit/Rrbs

Question

[simonconti]

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!

Answer 1

[simonconti]

I got the following link using the UCSC tables for a complete annotation of mm10 - is this correct?

http://genome.ucsc.edu/cgi-bin/hgTables?hgsid=330701821&boolshad.hgta_printCustomTrackHeaders=0&hgta_ctName=tb_refGene&hgta_ctDesc=table+browser+query+on+refGene&hgta_ctVis=pack&hgta_ctUrl=&fbQual=whole&fbUpBases=200&fbExonBases=200&fbIntronBases=200&fbDownBases=200&hgta_doGetBed=get+BED

[Rm]

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