how to generate .bed files for methylation (RRBS) analysis
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12 months ago
arshad1292 ▴ 70

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!

methylation • 413 views
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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?

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Entering edit mode
12 months ago
  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.

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