Question: DNA methylation analysis
0
gravatar for esraayassin
5.1 years ago by
esraayassin0 wrote:

hi every one,

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 alot,

esraa

next-gen • 2.0k views
ADD COMMENTlink modified 5.0 years ago by Larry_Parnell16k • written 5.1 years ago by esraayassin0
1

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.

ADD REPLYlink written 5.1 years ago by Devon Ryan91k

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

ADD REPLYlink written 5.1 years ago by esraayassin0

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

ADD REPLYlink written 5.1 years ago by Devon Ryan91k

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

ADD REPLYlink written 5.1 years ago by esraayassin0
2

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).

ADD REPLYlink written 5.1 years ago by Devon Ryan91k

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

ADD REPLYlink written 5.1 years ago by esraayassin0
1

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.

ADD REPLYlink written 5.1 years ago by Devon Ryan91k
1

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

ADD REPLYlink written 5.0 years ago by Neilfws48k
0
gravatar for Larry_Parnell
5.0 years ago by
Larry_Parnell16k
Boston, MA USA
Larry_Parnell16k wrote:

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.

 

ADD COMMENTlink written 5.0 years ago by Larry_Parnell16k
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