DNA methylation analysis

Question

[esraayassin]

Hi everyone,

I'm using genespring software for my analysis, I've downloaded the data from GEO in BED format and the software accept methylation data just in BAM or SAM format. how can convert the format from BED to SAM or BAM.

thanks a lot,

esraa

[Devon Ryan]

Why not just use a different tool? There's no obvious method for converting a random BED file into a SAM or BAM file, since they don't necessarily contain the same information.

[esraayassin]

thanks a lot Mr Devon Ryan, but i don't know any other tool and if you help me to find a tool i will be grateful for that

[Devon Ryan]

Which GEO dataset is it? You can undoubtedly do the analysis in R.

[esraayassin]

this is my data http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE17510 and i don't know how to use R

[Devon Ryan]

The GEO dataset that you're looking at is a MeDIP-ChIP experiment, so it'd be impossible to make a SAM or BAM file, which require a sequencing-based experiment rather than a microarray-based experiment.

It looks like this is an Agilent methylation array and that the raw files are available, so perhaps theres a package already available to do the analysis (I'm not familiar with Agilent methylation arrays, so I don't know what's out there).

[esraayassin]

ok thanks a lot but please can you check this http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28314

[Devon Ryan]

That's a MeDIP-seq experiment, so there are more tools for it, such as Batman and MEDIPS. I don't see alignments available, but you could generate them easily enough.

[Neilfws]

time to learn then :) it will be time well-spent

Answer 1

[Larry_Parnell]

Use MeDIPs or Batman for this type of dataset. These are standard tools, ones we've used here for our analysis of such data that we generated ourselves.