Question: Total CpG genome count
0
gravatar for rebekah_321
4 months ago by
rebekah_3210 wrote:

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

cpg bismark rrbs methylation • 297 views
ADD COMMENTlink modified 4 months ago by maxime.policarpo30 • written 4 months ago by rebekah_3210
1

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
ADD REPLYlink modified 4 months ago • written 4 months ago by cpad011210.0k

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

ADD REPLYlink written 4 months ago by maxime.policarpo30

I was meaning more is the programme suitable for this

ADD REPLYlink written 4 months ago by rebekah_3210

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

ADD REPLYlink written 4 months ago by Devon Ryan86k

A: How to find out total # of CpGs sites from a fasta file?

ADD REPLYlink written 4 months ago by Vijay Lakhujani3.2k

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

ADD REPLYlink written 4 months ago by rebekah_3210

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

ADD REPLYlink modified 4 months ago • written 4 months ago by Vijay Lakhujani3.2k

Refer to Emboss programs : http://emboss.sourceforge.net/apps/cvs/emboss/apps/newcpgreport.html, http://emboss.sourceforge.net/apps/cvs/emboss/apps/cpgreport.html and http://emboss.sourceforge.net/apps/cvs/emboss/apps/newcpgseek.html

ADD REPLYlink modified 4 months ago • written 4 months ago by cpad011210.0k

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

ADD REPLYlink written 4 months ago by rebekah_3210

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

ADD REPLYlink written 4 months ago by rebekah_3210

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

ADD REPLYlink written 4 months ago by rebekah_3210
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