Biscuit bed file import in RnBeads

[pawan upadhyay]

Hi 

I have generated by WGBS data bed files using biscuit tool. As per user manual, by default RnBeads does not seems to take biscuit output as input.

Therefore, I am wondering what is minimum info in bed file needed in order to be able to analyze using RnBeads? The following are the few lines of biscuit output bed file.

chr1	286144	286146	1	5	C:1.000:5,G:.:0
chr1	287925	287927	1	2	C:1.000:1,G:1.000:1
chr1	288098	288100	1	2	C:1.000:1,G:1.000:1
chr1	366387	366389	1	2	C:1.000:1,G:1.000:1
chr1	366418	366420	1	2	C:1.000:1,G:1.000:1
chr1	366423	366425	1	2	C:1.000:1,G:1.000:1
chr1	366433	366435	1	2	C:1.000:1,G:1.000:1
chr1	366509	366511	1	2	C:1.000:1,G:1.000:1
chr1	366514	366516	1	2	C:1.000:1,G:1.000:1

Any help will be highly appreciated.

Thank you

Pawan

[Michael Scherer]

Dear Pawan,

The minimum requirement for RnBeads import are the columns Chromosome, Start, End, Total Read Coverage and Number of Methylated/Unmethylated Reads. It seems as if this is not provided from the output you show. Could you try to generate a more detailed file as input?

As an alternative, you could convert your BED file into a DNA methylation data matrix, which you can directly feed into RnBeads. However, crucial preprocessing steps depending on the read coverage statistics will not be available then.

Best,

Michael