Saber HQ

Hi @waltergallegog ! Thanks for your interest in using NanoSim and reporting this issue. It is a bit hard for me to trace back the issue without running and testing...

Sorry for this late reply @dariober It is indeed very weird behaviour by NanoSim which I have never seen before. Have you tried using pre-trained models as well? Is the...

Thanks for reporting this @danpal96 In the `extract_reads` function of `simulatory.py` script, the `if` clauses are inside a `while True` loop. If the condition is met, `length < seq_len[s][key]`, then...

> So now i can consistently run nanosim. might be related to min and max length of reads im trying to simulate. Nice to hear that you were able to...

Hey @joyceFunk123 Thanks for your interest in using NanoSim. NanoSim uses the quantification file to choose transcripts to simulate reads from. It is an approximation estimation and does not reflect...

Hi @AntonS-bio Thanks for flagging this and for the detailed explanation — much appreciated. Your proposed solution is a smart and practical workaround. We'll make sure to address this more...

Hi @SimonHegele, Thanks for using NanoSim and bringing this issue to our attention. **To better assist you, could you please share how you quantified the expression profile for the reference...

You’re absolutely right @lcoombe —this is the key question, and it’s why I asked @SimonHegele for clarification earlier. Understanding how the expression file was created is crucial. Specifically, whether it...

Thanks for the clarification @SimonHegele Then, looks like there is a bug and we will look into it for sure. I suspect that is either related to the code lines...