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Old 08-07-2013, 01:34 PM   #1
Jim Michael
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Thumbs up methylation value and coverage

Dear all,

From bisulfite sequencing data (downloaded from NGSmethDB ) I've calculated some CpG sites showing that the number of their methylated cytosines (methylC) is more than the number of their corresponding coverages (numReads). Thus it will give the methylation value greater than 1.0. Is this a feasible solution? why?
my example is:
##########################################################
chrom chromStart chromEnd context numReads methylC meth
16144246 chr21 46872388 46872389 CG 27 28 _______ 1.0370370
16144370 chr21 46876524 46876525 CG 9 10 _______ 1.1111111
16144659 chr21 46887294 46887295 CG 13 9 _______ 0.6923077
16144722 chr21 46888779 46888780 CG 5 6 _______ 1.2000000
16144783 chr21 46890849 46890850 CG 5 6 _______ 1.2000000
16144875 chr21 46892957 46892958 CG 9 9 _______ 1.0000000
16144890 chr21 46893253 46893254 CG 18 18 _______ 1.0000000
16144898 chr21 46893401 46893402 CG 15 14 _______ 0.9333333
##########################################################

Thank you for the help!

Last edited by Jim Michael; 08-07-2013 at 11:59 PM. Reason: reformulation of the question
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Old 08-07-2013, 02:07 PM   #2
chadn737
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I don't understand the question.
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Old 08-07-2013, 03:34 PM   #3
PeteH
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You'll need to clarify your question, perhaps with an example of such a CpG.
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Old 08-08-2013, 01:30 AM   #4
dpryan
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You should alert NGSmethDB to the affected datasets, obviously there's something wrong with them. I actually just went ahead and downloaded one of their datasets ("bcell_cg_minRead10.txt") and found the same issue. You'd be best served by processing the experiments from the fastq files yourself.
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Old 08-08-2013, 04:57 AM   #5
Jim Michael
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Ok, thank you dpryan for the advice~
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Old 08-12-2013, 08:20 AM   #6
Jim Michael
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Quote:
Originally Posted by dpryan View Post
You should alert NGSmethDB to the affected datasets, obviously there's something wrong with them. I actually just went ahead and downloaded one of their datasets ("bcell_cg_minRead10.txt") and found the same issue. You'd be best served by processing the experiments from the fastq files yourself.
@dpryan, the bug has been corrected by them.
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