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MalteThodberg / CAGEfightR

Analysis of Cap Analysis of Gene Expression (CAGE) data using Bioconductor
GNU General Public License v3.0
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How to load custom non-model species genome #20

Open ckuanglim85 opened 3 months ago

ckuanglim85 commented 3 months ago

Hello, I have some CAGE sequencing data from oil palm. The reads were mapped to the genome. I have alignment BAM file, and converted into BigWig. I have problem running quantifyCTSSs because I couldn't define the genome parameter. How can I load this custom non-model species genome and use CAGEfightR? Thanks in advance.

MalteThodberg commented 3 months ago

Have you tried running if with genome = NULL? Then it tries to use the BigWig-files to figure out the genome.

Alternatively you can manually build the Seqinfo object needed for the the genome argument. See the ?Seqinfo from the GenomeInfoDb package on how to do this!