how to generate .bed files for methylation (RRBS) analysis

Question

[arshad1292]

Hello,

I am new to DNA methylation data analysis and I am using a pipeline that requires .bed files as input for analysis. However, I have raw pair-end fastq files (1.fastq and 2.fastq). How can I generate .bed files using these fastq data?

Many thanks in advance!

[ATpoint]

That cannot really be answered. BED is a format, not a fixed definition of what should be in there. So what shall be the content of that BED file? Is this a published pipeline with documentation?

Answer 1

[colindaven]

1. Align with bismark. If you can, use the nf-core methyl-seq pipeline. Else Bismark by itself.
2. Use the resulting BAMs and for example bedtools bamtobed to convert bam to bed format.
3. Read some existing methods sections !

This might get you started at least.