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Answer: Why cd-hit-est not work when sequence identity threshold<0.95？
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weidonglu
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The reason for your problem was most likely due to you relative complex data and too little system memory. For 20000-30000 transcriptome se…
Comment: Perfom a Gene Ontology Analysis from GO terms txt file
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sansan_96
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Your table should look like this (GO terms):
```
geneid GOid
Zm00001eb000010 GO:0003690;GO:0003727;GO:0019843;GO:0005739
Zm00001eb000020 G…
Answer: Perfom a Gene Ontology Analysis from GO terms txt file
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sansan_96
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I understand, here is an example with topGO where you need a differential expression table (DESeq2 for example) and a table of GO terms:
`…
Comment: Perfom a Gene Ontology Analysis from GO terms file
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Hamtaro
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Thank u for your reply. The problem is that I used the genome and gene annotation from that webpage, not ensemble or ncbi, so I have to use…
Comment: Perfom a Gene Ontology Analysis from GO terms file
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sansan_96
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Hello,
To perform functional enrichment analysis there are packages such as topGO or clusterProfiler that can work very well. Lately I've …
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LChart
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The anti-diagonal band does suggest some fraction of genotypes are strand-flipped - probably G/C or A/T variants.
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Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the cod…
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Thank you! I need this for eukaryotic organism and known protein sequences, but I guess seqkit would work well!
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Paper referred to in question: https://pubmed.ncbi.nlm.nih.gov/29195078/
> so I want to understand how you reduced the 12063 genes to 978…
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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…
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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…
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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…
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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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