Entering edit mode
7.8 years ago
wanziyi89 ▴ 60
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?
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.