Hi everyone!
(I'm hoping you're all safe and healthy)
I could really use some help figuring out how to remove the bad nucleotide symbol "???" in my Geneious sequence. (See attached photo)
Before the apocalypse began, my lab had just finished finding the WGS of all 72 ECOR Library strains. My Lab Manager assembled them using a local supercomputer (de novo), but the FASTA file of the assembled sequences all contain long stretches of "????????" where there were bad reads. When you try and search within these files, they'll bring you to a stream of "????" and when you push the "Next" button on the search menu, it will bring you down the stream of "?????" marks, one "?" at a time. Brutal...
Any idea of to completely delete these "?" marks? I have a Mac laptop, but I tried to replace "?" with "N" but when imported, it turns the marks back to "?". Any suggestions?
Thank you very much,
Emma Farquharson
Nugen Lab
Cornell University
Hey Emma! Do you need only to remove these "?" from your fasta file? If so open it in some text editor e.g. Notepad++ and there ctrl+f -> replace... and there you fill what you need to replace and with what (could be blank) and press replace all.
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