Annotating peak using Chipseeker for non-model organism
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4 months ago
Assa Yeroslaviz ★ 1.8k

I have a chip-seq data analyzed using macs3 to get the peak files. I would like to annotate those files using the ChIPSeeker package. Unfortunately, I'm working aon an organism without a TxDB or org*.db packages.

I know I can create a TxDb object from a GTF file using the GenomicFeatures:: makeTxDbFromGFF function.

The function annotatePeaks needs though an annoDB object (like org.Hs.eg.db for the human genome).

Is there a way to create this object from scratch? If so, what files does one needs to have for that?

thanks

Assa

GenomicFeatures chipseq chipseeker annoDB TxDb • 317 views
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You don't actually need to provide the annoDB object, it's optional. Most of the extra information it would have added is present in the GTF file to, so you can just merge the information into the results after you run the function.

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