Comments (3)
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.
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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.
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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.
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Related Issues (20)
- Add a detection method for unintended inversion HOT 3
- Add VCF reports
- Improve Handling of Sequence Error Deletions within Large Deletions HOT 1
- Replace setup.py to pyproject.toml HOT 3
- GUI implementation HOT 3
- DAJIN2 reports extremely low-frequency alleles (e.g. 0.005%) HOT 1
- Test for Dorado basecaller HOT 3
- Add tests to `utils.cssplits_handler.insertion_within_deletion` HOT 1
- An error occurs if there is an "_" in the FASTA header name. HOT 1
- Incorrect Insertion Allele Judgement for Matched Sequences within Large Deletions
- Test with Python 3.11 and 3.12 HOT 2
- Enhance Alignment Accuracy for Short Reads by Integrating `map-ont` and `splice` Options HOT 1
- Test DAJIN2 using the Build mappy on macOS ARM HOT 3
- Remove `networkx` from pyproject.toml HOT 1
- Add alignment chart
- Remove `pandas` from pyproject.toml
- Modify `convert_cssplit_to_dna`
- Replace `typing.Generator` to `collections.abc.Iterator`
- Replace `midsv` to `csvtag` HOT 1
- Add `sr` presets to all execusions
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