The best data format for to store BS-seq or RRBS dataset

Question

[Shicheng Guo]

Hi All,

Is there any suggestion which kind of intermediate data format would be nice to be use to save the BS-seq or RRBS dataset?

Fastq? Bam? MethylFreq? wig? bedgraph?

Thanks

Answer 1

[Devon Ryan]

I usually keep (A) BAM files and (B) bedGraph files (though I gzip them). One could probably use hdf5 in place of the bedGraph files and save some space/improve performance, though I've never tried.