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genome.ref is not a gtf #4

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johnchamberlin opened this issue Jan 30, 2024 · 0 comments
Open

genome.ref is not a gtf #4

johnchamberlin opened this issue Jan 30, 2024 · 0 comments

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@johnchamberlin
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Hello,
I am trying to use infernape on some human data. The documentation indicates I should pass a gtf to parameter genome.ref, but the example genome.ref file 'ref.csv' is not a GTF:

head ~/Downloads/ref.csv
,chromosome,feature,start,end,strand,gene_symbol
1,chr11,transcript,51685386,51688653,-1,0610009B22Rik

The function which imports genome.ref also appears not to expect a gtf:

ref.df = utils::read.csv(genome.ref)
Do you suggest I parse my GTF into the given format?

Thanks,

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