Question: BEDgraph to BED/bam
0
gravatar for wanziyi89
4.8 years ago by
wanziyi8960
Singapore, Temasek Life Sciences Laboratory
wanziyi8960 wrote:

Hi guys,

 

Any tools or software available for converting bedgraph to bed and then to bam?

I would like to extract CpG methylation calls using bismark and then save them in Bam format then convert them to bam using bedtools.

I saw some references to manually convert bedgraph to bed via UNIX commands, just wondering is there any tools to directly do the job?

bed • 3.7k views
ADD COMMENTlink written 4.8 years ago by wanziyi8960
2

It's not clear how one would store the information in a bedGraph file as a BAM file. Certainly the interval is trivial to encode, but BAM files aren't intended to convey arbitrary decimal scores like bedGraph. Why not use a bigWig file instead? It's binary like BAM files and can be loaded similarly in genome viewers and has the benefit that it's actually intended to hold information like this.

ADD REPLYlink written 4.8 years ago by Devon Ryan95k
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