I have a bunch of bedgraph files with very little annotation information, and I have no idea whether the data was generated from whole genome or targeted bisulfite sequencing. What is the best way to determine this?
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biohack92
2 answers
Open the files in IGV and check if the reads align to the whole genome or to only a subset of the genome (e.g. the exome)?
What exactly is the bedgraph data describing? Coverage? What is the range of the data? If the scores are between 0-1 or 0-100 with a bimodal distribution then maybe it's methylation data. Otherwise from a bedgraph file it's going to be hard to determine. I'd say take a look at a histogram of values. If they're Poisson distributed then it's probably counts from uniformly distributed data such as aligned WGS reads.
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