tools to identify the sequencing depth for CpG islands in methyl seq.

Question

[vsivaranjanipriya]

Hi all,

I am new to NGS data analysis..

Can anyone suggest me how to determine the sequencing depth for CpGs in Methyl Seq data..

Thanks in advance..

[brentp]

have you looked at bedtools coverage or featureCounts?

[iyer.laxman4]

Can you please elaborate how to use featureCounts

Answer 1

[Matt Shirley]

Try using "bedtools coverage" in a manner similar to what Stephen Turner does in this post, but substitute a BED file of CpG island regions instead of exome capture targets. For CpG island regions I like using these from the Irizarry group.