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Recent Replies
Comment: Landmark gene selection in L1000.
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GenoMax
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> so I want to understand how you reduced the 12063 genes to 978 genes
From the paper:
> Gene space summary
>
> The L1000 assay directly…
Comment: Landmark gene selection in L1000.
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GenoMax
141k
Paper referred to in question: https://pubmed.ncbi.nlm.nih.gov/29195078/
Comment: Batch effects : ComBat or removebatcheffects (limma package) ?
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cwwong13
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@kevin May I know whether your comments and edits were mainly based on the fact that "Previously, [crazy] people had been using the origina…
Comment: Programmatically retrieving positions of protein active site residues
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Wayne
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Wow, I was shocked at this AI answer that looks to be a good start for using UniProt. Sharing it in case it is useful. (It will work in ses…
Comment: NGS forensics: how to know if data is fabricated
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noodle
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> Can you clarify what you mean by "100% of reads pass cutadapt, even
> though 70% of reads contain adapters and get trimmed.
The header o…
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If you have independent information available (e.g. genotype data for both individuals) then you *may* be able to assign reads based on the…
Answer: Extract protein sequence
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You didn't mention what kind of organism you are working with and what kind of protein you are looking for?
If it happens to be a microbia…
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pairedttest
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Thank you Gordon for your expertise. One question that I have now that I have a list of DE genes is how to interpret logFC of this continuo…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
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salias
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Yes I plan to use QIIME2, but I'm Cutadapting outside QIIME so its easier to MultiQC without importing/unzipping QZAs (and QIIME2 importing…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
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GenoMax
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> 3' adapters were removed aprox. 90 times each one, so there sohuld not be read-through at all here
Then you have data that has poor Q sc…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
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salias
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Following your advice, I checked the primer and adapters sequences and edited the question accordingly
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dsull
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We can't phase them out per se, because ``kallisto index`` is still the engine responsible for creating the index under the hood (and there…
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"./." in your gVCF files typically indicates a lack of information or uncertainty about the genotype at that particular position.
This co…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
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salias
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Fungal ITS2 region (length is really variable so read-through can be an issue)
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