featureCounts - cannot select a built-in genome

rna-seq

#1

I am trying to use featureCounts on an unpaired collection of 9 bam files in my history. For the “Gene annotation file” section, I selected “featureCounts built-in”. However, I can’t select the genome build I want (mm10).

How is this possible? The menu just doesn’t pop down. When I imported these BAM files, I did not specific their build at the time, in the the “Genome (set all):” setting. Is that why?

Thanks


#2

If your genome is either hg38, hg19, mm10, or mm9 -> use featureCounts built-in option in Gene annotation file. You may need to set genome build for your BAM files (in the image below it is set to hg19. If it is not set you will see ?)

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