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Mob-typer returns different results when plasmids were rotated. #85
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It would be helpful if someone could tell me this issue is reproducible or not. Thank you, |
I finally found the reason for this. |
There seems to be some issues with blast and length of headers. I have implemented a fix in 3.1.0 where all sequences are renamed internally for all of the blast and search calls. Then reported back as the original sequence identifiers. |
Hi,
Thanks for developing this nice tool!
I got different results for the same plasmid using MOB-typer.
When I ran
mob_typer --multi --infile KX912253_RC.fasta --out_file KX912253_RC.tsv
, I got the results as bellow (no plasmid replicons, relaxase, mpfs detected):However, when I rotated the plasmid and ran
mob_typer --multi --infile KX912253_RC_rotated.fasta --out_file KX912253_RC_rotated.tsv
, I got the following results (now plasmid replicons, a relaxase, and mpf were detected):I thought the results can slightly be different after the rotation since rotation can recover a broken gene (i.e., if the gene spans the beginning and end of the contig, this gene can be recovered by the rotation).
However, the results are completely different in this case and most genes used for the typing seem to be intact before the rotation.
I've attached fasta files of the plasmid before/after the rotation. (the file extension is .txt since github does not allow me to attach files with .fasta)
KX912253_RC.txt
KX912253_RC_rotated.txt
If you have any ideas, please let me know.
Thank you,
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