How to filter gff based on certain gene list in rtracklayer?
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alslonik • 0
@alslonik-15194
Last seen 3.7 years ago

Hi,

I am trying to understand whether the filter option is able to filter the gff that I have based on list of gene IDs, along with their exons, CDS, mRNA and UTR.. Is there an option like this in the package? If not, any idea how to do it? I am using simple grep for now, but it has its problems and I would like to know if there is smth quicker and clearer in R..

rtracklayer gff filter • 559 views
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@michael-lawrence-3846
Last seen 10 months ago
United States

I think you could just import() the file, subset the returned object by whatever criteria, and export() it back to the file.