Question: Calculating GC content of all CpG islands
1
gravatar for Baby Bioinformatician
12 months ago by
Moscow
Baby Bioinformatician90 wrote:

Hi Biostars, I have two files containing the genomic ranges of all CpG islands and promoter sequences of Human genome hg19. I would like to do an association test between CpG islands and promoters. So I need to calculate the GC contents of the two files. However, I am not conversant working with genomic coordinates. Could somebody please help with a command that I can use to calculate the GC contents of the two files. Thanks.

ADD COMMENTlink written 12 months ago by Baby Bioinformatician90

Please use the search function. One approach is to get the sequences of the coordinates using bedtools getfasta and then use e.g. How To Calculate A Region‘ Gc Content In Reference Genome??

ADD REPLYlink written 12 months ago by ATpoint34k

Hi

If you are using R; can try seqinr package. On that you could find function "GC" and can do whatever you are looking for.

ADD REPLYlink written 12 months ago by archana.bioinfo87180
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