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

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

rrbs bs-seq

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updated 4.0 years ago by Ram

• written 10.7 years ago by Shicheng Guo

1 answer

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.

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written 10.7 years ago by Devon Ryan

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