Originally posted by bruce01
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First allow me to paste a passage from the User Guide:
The methylation call string contains a dot ‘.’ for every position in the BS-read not involving a cytosine, or contains one of the following letters for the three different cytosine methylation contexts (UPPER CASE = METHYLATED, lower case = unmethylated):
Code:
z unmethylated C in CpG context Z methylated C in CpG context x unmethylated C in CHG context X methylated C in CHG context h unmethylated C in CHH context H methylated C in CHH context u unmethylated C in Unknown context (CN or CHN) U methylated C in Unknown context (CN or CHN)
Can't you just take the BAM file and use this to do copy number analyses? Using the coordinates of the read alignmnents you can relatively quickly extract the fully unconverted sequence from the reference genome (is this the pre-bisulfite state?), or go back and extract the bisulfite sequence as it comes from the sequencer out from the FastQ file (e.g. based on the read ID). Does this answer your questions?
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