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Recent Replies
Comment: Resolving over clustered NGS with Q-scores
by
ATpoint
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Has phiX been spiked in to increase nucleotide diversity.
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SplitInf
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since this is one of the top search results, I'm cross-posting this comment from another user (alexbarrera)
"that the values of the 5th co…
Comment: Very low successfully assigned alignments with feature counts
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Load up your data in IGV and visualize it relative to your annotation file. It will tell you where the data aligns.
5% match on a 99% ali…
Answer: Ambient RNA removal method that generates whole (integer) counts
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I've definitely just rounded soupX output and had no issues with pseudobulking.
A colleague speaks highly of Cellbender, though it take…
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I thought Interproscan already has species-specific information, for example [this][1] page for Buchnera aphidicola. You can try to search …
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I don't understand your problem. What do you mean when you write:
> These genes even in the same species may use different genetic codes.
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I also encountered issues when running ballgownrsem with gff files. Ballgown object was created, there is no informations about TPM and FPK…
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I had the same problems and then realize that I forgot the preprocessing!
If you add this commands before running the PCA, it should work:…
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Try tripling your example seq length, see 20bp min region
-l INT min region length to output [20]
To answer your question, it …
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Is the genome/annotation from the same source i.e. Ensembl or so it appears?
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What does this do? It's not documented well and does not work for me in terms of, it produces no output:
cat foo.fa
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Did you not see the last part in my comment above about how to get the sequence?
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Thank you for your response.
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The main one I use is stats.sh from the bbmap package (conda installable).
GC is 0.428 = 43% in this example. It's very quick.
stats.sh M…
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