Closed ngroberts closed 2 years ago
Hi Nick! I see you have gaps in your alignment. Could you re-run the query with the gaps removed? I'll send you a script for dealigning sequences via email.
Hey Felix! I can use unaligned sequences! And I can remove gaps. I will update you how it shakes out.
Cheers,
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From: Felix Thalén @.> Sent: Friday, June 10, 2022 12:03:32 PM To: fethalen/Patchwork @.> Cc: Nick Roberts @.>; Author @.> Subject: [EXTERNAL] Re: [fethalen/Patchwork] Patchwork error after alignment trimming. (Issue #35)
Hi Nick! I see you have gaps in your alignment. Could you re-run the query with the gaps removed? I'll send you a script for dealigning sequences via email.
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For future reference, gaps in the alignment was indeed the problem. In the future, I will try to implement gap-removal and or a warning message for this issue. Until then, please remove your gaps!
Hello,
I am doing a test of patchwork using a genome assembled in SPades as a query with a large ortholog set as a reference. Patchwork shoots me an error after the alignment trimming step I cannot diagnose.
My reference is formatted as:
My query is formatted as:
Any help would be appreciated.
Cheers, Nick