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Recent Replies
Comment: I cannot download VG in any way
by
Ram
44k
In that case, OP should have said "Cannot install SequenceTube", since that is the problem, not vg.
Maybe this is the SequenceTube that OP…
Comment: I cannot download VG in any way
by
GenoMax
142k
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…
Comment: I cannot download VG in any way
by
Ram
44k
> 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…
Comment: I cannot download VG in any way
by
Ram
44k
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…
Comment: Can I count UMI-barcode combination without mapping?
by
GenoMax
142k
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…
Comment: Best practices in Fungal Genome Assembly
by
samuel.a.odonnell
▴
540
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 …
Comment: I cannot download VG in any way
by
GenoMax
142k
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…
Comment: Best practices in Fungal Genome Assembly
by
Umer
▴
50
Hi, Thanks for your suggestions.
> polish the long-read assembly afterwards
Previously, I used Pilon for polishing and i did 10 rounds. (…
Comment: How do I check if a DNA sequence of a gene is supported by RNAseq data?
by
Jack
•
0
I have the DNA sequences of every phase variable locus in the genomes of 8 bacterial isolates.
Repeats range from polyG tracts around 9-20…
Comment: Best practices in Fungal Genome Assembly
by
samuel.a.odonnell
▴
540
For the short-read strains: <br/>
I would recommend just using SPADES
For the strains with long-reads: <br/>
I think spades and masurca as…
Comment: txt file to bigwig
by
GenoMax
142k
Click on `edit`. That should open the edit window which will have a `Delete` button at bottom right to delete the comment/reply.
Comment: UMI-Tools knee-method has great influence on the results of white list
by
Assa Yeroslaviz
★
1.9k
Can you pls make it an answer so that I can accept it? thx
Comment: Best practices in Fungal Genome Assembly
by
samuel.a.odonnell
▴
540
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…
Comment: txt file to bigwig
by
sogand
•
0
Hi, I tried to delete my comment but can't see any delete/remove option here!
Thanks
Comment: Error with pheatmap - 'from' must be a finite number
by
Ram
44k
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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