This is a test version of Biostars. For the public version, visit https://www.biostars.org.
Total CpG genome count

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
• 5,098 views • link
updated by maxime.policarpo maxime.policarpo • written by Baylie_321 • Baylie_321

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

• 1 views • link
written by maxime.policarpo maxime.policarpo

I was meaning more is the programme suitable for this

• 1 views • link
written by Baylie_321 • Baylie_321

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

• 1 views • link
written by Devon Ryan Devon Ryan

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

• 1 views • link
written by Baylie_321 • Baylie_321

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

• 1 views • link
written by lakhujanivijay lakhujanivijay

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

• 1 views • link
written by Baylie_321 • Baylie_321

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

• 1 views • link
written by Baylie_321 • Baylie_321

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

• 1 views • link
written by Baylie_321 • Baylie_321

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"))

7
• 1 views • link
written by cpad0112 cpad0112

0 answers

No answers yet.

Log in to answer this question.

More posts like this