Question: Calculating GC content of all CpG islands
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gravatar for Baby Bioinformatician
5 weeks ago by
Moscow
Baby Bioinformatician40 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 5 weeks ago by Baby Bioinformatician40

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 5 weeks ago by ATpoint17k

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 5 weeks ago by archana.bioinfo87120
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