Simulate (targeted) sequencing of single genes

[FreekManders]

Hi,
I'm trying to simulate reads for individual genes. However I noticed that after aligning, the read depth in the first few hundred and the last few hundred bases of each reference sequence is lower than in the rest of the references. I tried using the amplicon method, but then I only have reads aligning to the beginning and end of my reference. It would be great if it was possible to simulate reads, so that you get a truly uniform read depth across the entire reference sequence.

[StefanLelieveld]

Hi Freek,

If this issue is still relevant, could you provide more details? Would it be possible to provide input-data and settings to reproduce this issue?