Moderator: Asaf
Asaf ♦ 8.4k
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Posts by Asaf
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... They might be separated by PC3, who knows. Since the first PC is separating the two outliers than the rest, removing them should change the PCA and you might get a separation. Even if not, you shouldn't remove these samples. ...
written 19 days ago by
Asaf ♦ 8.4k
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... The two allergic samples on the far right look suspicious, I'm sure that removing them will result with a better-looking PCA plot, you should try to understand what makes them so different than the rest of the samples. ...
written 19 days ago by
Asaf ♦ 8.4k
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Comment:
C: Defining groups in Geo2R
... Yeah, that's weird, it only has the M9 replicates. You should probably email the corresponding author and ask them. ...
written 20 days ago by
Asaf ♦ 8.4k
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Comment:
C: Hypothetical protein in Prokka
... You can use eggnog-mapper http://eggnog-mapper.embl.de/ to assign each protein an EggNOG orthology group, it's not being used with prokka. ...
written 29 days ago by
Asaf ♦ 8.4k
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... In my experience too. ...
written 5 weeks ago by
Asaf ♦ 8.4k
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... Assembly is an art, usually the default works good. Anyway I would use an established pipeline like https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1007134 or https://github.com/nf-core/bacass ...
written 6 weeks ago by
Asaf ♦ 8.4k
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... I think that sva is your go-to in this case unless you think there is a specific effect for methylation that is more nuanced that will make a surrogate effect act differently on this data. Since you only have processed data I think you'll be good with that. ...
written 7 weeks ago by
Asaf ♦ 8.4k
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... I'm guessing an empty line in a bed (?) file.
Try actually explaining what was the input and the error. ...
written 7 weeks ago by
Asaf ♦ 8.4k
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... I guess you can use a bash script to do that. Something like:
for f in */contigs.fasta; do cp $f /destination/dir/${f%/contigs.fasta}.fasta; done
The `%` removes the following text from the variable so the contigs.fasta will be changed to the folder name.
(I didn't test it but it should work) ...
written 8 weeks ago by
Asaf ♦ 8.4k
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