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Recent Replies
Comment: I cannot download VG in any way
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In that case, OP should have said "Cannot install SequenceTube", since that is the problem, not vg.
Maybe this is the SequenceTube that OP…
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I read that to mean that the only way they were able to download `vg` was by using `conda`. Since `SequenceTube` (whatever that is) require…
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> The only way that I managed to download vg is using conda, however since my primary goal is to download SequenceTube
You're mentioning t…
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Also, OP buries the lede and uses a misleading title. They are able to install vg using conda, but that is secondary to them using a differ…
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You can use some code I have here for inspiration: https://www.biostars.org/p/270737/#270753
You can extract the UMI by using.
$ awk…
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I think 10 rounds in excessive. I usually only run 1-3 rounds (as long-read accuracy has improved I have used fewer and fewer rounds), but …
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Why are you not downloading the `vg` binaries provided here: https://github.com/vgteam/vg/releases/tag/v1.57.0
Use the `Click here to Downl…
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Hi, Thanks for your suggestions.
> polish the long-read assembly afterwards
Previously, I used Pilon for polishing and i did 10 rounds. (…
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I have the DNA sequences of every phase variable locus in the genomes of 8 bacterial isolates.
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Comment: Best practices in Fungal Genome Assembly
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For the short-read strains: <br/>
I would recommend just using SPADES
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I think spades and masurca as…
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Click on `edit`. That should open the edit window which will have a `Delete` button at bottom right to delete the comment/reply.
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Assa Yeroslaviz
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Can you pls make it an answer so that I can accept it? thx
Comment: Best practices in Fungal Genome Assembly
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I think tools like quickmerge (or Ragtag's patch command) can help for long-read assemblies, but I would definitely avoid using them with s…
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Hi, I tried to delete my comment but can't see any delete/remove option here!
Thanks
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You'd see a different issue if the vector being analyzed contained character entries. This is clearly a problem with NA/NaN/Inf values in t…
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