Annotation using different database

[jennyp76]

Hi,
First of all, thank you for the wonderful tool. It been a lot of help.

I am trying to compare the total copy number between PureCN and CNVkit based on genes.
So, comparing the total copy number of a gene detected from PureCN and CNVkit.
Therefore, keeping the database used for annotation should be the same.

1. Would there be a method to annotate genes using the 4th column of the BED file instead of TxDb.Hsapiens.UCSC.hg38.knownGene R package?
2. And it this "https://hgdownload.soe.ucsc.edu/gbdb/hg38/knownGene.txt" is the annotation file used in PureCN for annotation?

Thanks, jen

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[lima1]

That's a valid feature request. I'll see when I have time for this. If urgent, you probably for now are faster correcting the interval file gene column manually.