Question about ASE calculation

[xtmgah]

Hello:

We are preparing a manuscript and want to use the same method to show the correlation between log2aFC and ASE-based estimate (similar to figure 5 b/c in Genome Research paper). We currently already calculated the log2aFC using eQTL data (fastQTL input files). So, can you let us know how to calculate the ASE-based estimate, and then we can calculate the correlation? Thanks. If you can provide a script to do this, it will be very helpful to us. We will cite your paper in future publication. Thanks.

[secastel]

I apologize for the extreme delay - I just saw this. I'm sure this is long past being useful, but to calculate aFC for ASE data is straightforward: log2(alt_count/ref_count). You will likely need to add a pseudocount of 1 to both alt and ref counts in order to prevent division by 0 errors.