Shan Yu - 2021-04-05

Hello Dr. Ye,

I didn't get how to treat several groups with biological duplications. I got 32 samples, including 5 healthy controls, 6 DieaseⅠ and 21 Dieas Ⅱ samples.
According to your manual(predictAPA -i Sample1.bedgraph Sample2.bedgraph -g 2 -n 1 1 -u hg19.utr.bed -o output.txt), I run this:
predictAPA -i Sample1.bedgraph Sample2.bedgraph …… Sample32.bedgraph -g 3 -n 5 6 21 -u hg19.utr.bed -o output.txt
The bedgraph files were ordred by sample types, but I'm not sure if the script was right, and I don't know how to do with deAPA :
deAPA(input_file, output_file, group1, group2, least_qualified_num_in_group1, least_qualified_num_in_group2, coverage_cutoff)

Or should I process 3 groups respectively in predictAPA steps ? If so, the predicted PA sites will be not uniform.

Looking forward to your reply. Many thanks~

Shan Yu