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rraadd88 / beditor

A Computational Workflow for Designing Libraries of sgRNAs for CRISPR-Mediated Base Editing, and much more
GNU General Public License v3.0
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no guide designed in the 05_output folder for test dataset #7

Closed leejimmy93 closed 5 years ago

leejimmy93 commented 5 years ago

Hi, I am now running beditor on the test dataset. It seems worked correctly by using the .yml parameter come with the test dataset. However, in the 05_output folder, there is no guide designed. Instead, it looks like this:

genome coordinate nucleotide mutation nucleotide wild-type guide: id guide+PAM sequence beditor score alternate alignments count CFD score length of polyT stretch 0 9:34111967-34111967- A A
1 9:34089056-34089056+ A G
2 2:50199638-50199638- A A
3 12:33484358-33484358+ A T
4 24:22070190-22070190- A T
... (this is danio_rerio test dataset, I don't think I get the result I am expected)

Can you please give me a hint about where I am possibly wrong? Also I think it would be helpful to include the correct output file in the test_dataset so people can get an idea on whether they get beditor work or not. Thank you in advance for help!

rraadd88 commented 5 years ago

Hi @leejimmy93, I'll get to this issue in a while. I've been strangled in some urgent stuff right now. :) On a cursory note, I feel that there is a mismatch between the genome installed by the pyensembl and the one downloaded by beditor. This should not happen ideally, as the genome versions are assigned very strictly. But I would not rule out the possibility that there could be some discrepancies in the genome database itself. Thanks for letting me know of this issue.