Calculating GC content of all CpG islands

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5.0 years ago

Baby Bioinformatician ▴ 100

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.

Genomic coordinates alignment gene GC content • 1.5k views

ADD COMMENT • link 5.0 years ago by Baby Bioinformatician ▴ 100

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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 REPLY • link 5.0 years ago by ATpoint 81k

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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 REPLY • link 5.0 years ago by archana.bioinfo87 ▴ 210

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