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

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..

sequencing
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updated by Ram Ram • written by vsivaranjanipriya • vsivaranjanipriya

have you looked at bedtools coverage or featureCounts?

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written by brentp brentp

Can you please elaborate how to use featureCounts

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written by iyer.laxman4 • iyer.laxman4

2 answers

ok please koi toh batao.

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written by iyer.laxman4 • iyer.laxman4

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.

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updated by Ram Ram • written by Matt Shirley Matt Shirley

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