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Many thanks !
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> I have access to both the raw reads and the previously assembled transcriptome submitted to TSA.
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> I am trying to determine wheth…
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There are a few factors to consider:
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If there is a high quality chromosome level assembly,…
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Pls add the output and your system (especially RAM), no one here can guess.
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There are software packages for power analysis such as https://academic.oup.com/bioinformaticsadvances/article/5/1/vbaf150/8173951.
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Run QC for each sample separately, then merge run SCTransform, PCA, then Harmony, UMAP, FindNeighbors and FindClusters.
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Thank you for the quick answer.
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I checked the memory before executing this command. I made a bash script on Ubuntu to run it on 15 folders. But, this problem happened in f…
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Many proteins have multiple domains, and are correctly classified with multiple KO numbers. That's not a bug in `kofam_scan` but rather a r…
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Thanks, I had completely forgotten that METABOLIC works with protein sequences. That will work :)
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It is easy to install `kofam_scan` and get the output:
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take a look at thomas winkler's stuff: https://www.nature.com/articles/nprot.2014.071
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Thanks for sharing this. I was able to get makeref to work.
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I am still confused how to put all predicted genes into metabolic pathways, I used eggnog-mapper for the prokka output, and can't find a to…
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