How to generate a scatter plot of duplication level vs log2reads per kilobase for RNA-seq? (seqmonk)

Question

[salamandra]

i wanted to generate a graph with Duplication level (%) vs Log2 reads per kilobase for an RNA-seq sample, as shown here. I managed to import genome, data and annotation files. But how to generate the graph?

From reading the manual seems I have to first do some probes (select genomic regions of interest) and then do quantitation. But where is the option to calculate duplication level/Log2 reads per kilobase?

And then how to build the plot?

Answer 1

[Andrei Poplaukhin]

Hello

Old but unanswered question. Maybe useful for someone

First of all you need to quantitate your data. Watch official Babraham youtube channel if you don't know how to do it:

https://www.youtube.com/user/BabrahamBioinf/videos

Once you have quantitated data, push plots -> Duplication plot. That will do the trick.

Cheers!