Open takeiga opened 3 months ago
I appreciate your reports!
As you mentioned, I've updated genome_fetcher.py
to ensure a perfect match between the control sequence and its reference. Consequently, there's a possibility that your control sequence in actc1L_cont_knockin.fa
might not align with the reference. Could you possibly share your control sequence in actc1L_cont_knockin.fa
? I'd like to examine the cause of error using your control sequence if possible.
I confirmed run completed successfully when I replaced older genome_fetcher.py, so it may come from updated one.
I am pleased to hear this. Your feedback is greatly appreciated! Thank you for your valuable contribution.
Our control sequence data is derived from the latest version of NCBI's Xenopus laevis reference genome (Xenopus_laevis_v10.1). But I used old ref genome, UCSC's xenLae2 for DAJIN2 prerequisite and those two different version of the genome contains nucleotide differences. So I understood the reason why the genome_fetcher.py showed error and will use UCSC's data if needed. I personally hope we can use NCBI data for reference data in further update of DAJIN2 if possible.
Thank you for your description! I'll rethink the method for obtaining genome coordinates. It might take some time, but I'll share the information here once it's updated.
After updating to 0.4.3, genome_fetcher.py reported error:
I confirmed run completed successfully when I replaced older genome_fetcher.py, so it may come from updated one. Thank you for your effort, anyway!