Total CpG genome count
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3.4 years ago
Baylie_321 ▴ 30

Hiya, I'm trying to get a total count of all CpGs present in a non-model organism genome. I have used bam2nuc in bismark to count dinucleotides - am I correct in thinking the count of CGs will be the total CpG count of the genome?

Best wishes,

Rebekh

RRBS Bismark Methylation CpG • 2.2k views
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If you want to count only CGs from fasta (nt) in R:

library (Biostrings)
data(yeastSEQCHR1)
yeast1 <- DNAString(yeastSEQCHR1)
dinucleotideFrequency(yeast1)['CG']
 CG 
7089

in python:

s = 'ATATTGCGAAAGAACGTAATTTTATCGAAAAATCGATGTcgcgcg'
print(s.upper().count("CG"))

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Couldn't you also count GCs nucleotides as it will be a CpG on the reverse strand ?

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I was meaning more is the programme suitable for this

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A GC is a GC on the other strand, not a CpG.

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Cheers :) I'll give the C program a go!

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Hello rebekah_321,

Don't forget to follow up on your threads.

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.

Upvote|Bookmark|Accept

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I tried emboss - but doesn't it just report CpG islands?

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Yes I have used emboss to predict CpG islands - now I want all CpGs not just islands

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Yes I have used emboss to predict CpG islands - now I want all CpGs not just islands

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