Multiple files for each sample in bisulfite sequencing dataset
I have a bisulfite sequencing dataset that have been aligned and consists of two experimental groups. Each sample has four bedgraph files named in the following manner:
sample1_plus_meth.bedgraph
sample1_plus_unmeth.bedgraph
sample1_minus_meth.bedgraph
sample1_minus_unmeth.bedgraph
Why were these files split in this manner, and is there a specific purpose for it? Is there a way to calculate relative methylation and then compare the two experimental groups together?
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Antonio R. Franco
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biohack92
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biohack92
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What tool produced that output? That's a rather annoying format to deal with, though I guess it allows them to convey all of the information without creating a new format (they could have also done that with two files, but oh well).
Can you show use the first couple lines of each file? It'd allow us to ensure that the last column is an integer value.