User: antonioggsousa

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Posts by antonioggsousa

<prev • 79 results • page 1 of 8 • next >
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Comment: C: running blastp on Ubuntu, Argument "query" file is not accessible error
... Hi, If you want to see where `blastp` was installed (assuming that you've a system installation rather than local), you can just type the following command on your shell: which blastp Though your problem does not seem related with the installation of `blastp`, but it seems related with the ...
written 8 hours ago by antonioggsousa480
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Comment: C: METAPHLAN: Getting genus level resolution but not family level
... This seems to be related with the taxonomic database used for the taxonomic profile with `METAPHLAN`. Which database did you use? Do you know? Sorry, but I never use myself. António ...
written 8 hours ago by antonioggsousa480
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Comment: C: Softwares for statistitical analysis of MetaPhlAn output
... Hi, Not sure. From the error it seems related with the fact that for that particular taxonomic annotation you got something annotated at genus level - `g__Gemella` -, but not annotated at family level `f__Bacillales_unclassified`, that is a higher rank just above the genus. This is quite strange, b ...
written 8 hours ago by antonioggsousa480
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Answer: A: Softwares for statistitical analysis of MetaPhlAn output
... Hi, You might want to try to use [STAMP: Statistical analysis of taxonomic and functional profiles](https://beikolab.cs.dal.ca/software/STAMP). It is the only GUI software that I know that may help to perform statistical analyses on taxonomic and functional data tables. Please read the user gu ...
written 1 day ago by antonioggsousa480
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Answer: C: heatmap in R
... Hi, Assuming in your last line, that the **a** before the `heatmap()` function is a copy/paste mistake, the error that you got is related with the fact that you're trying to index columns that are outside the range of your matrix. What this means is that `geneExp_matrix` matrix does not have 317 c ...
written 2 days ago by antonioggsousa480
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Comment: C: RStudio Pheatmap: sort DEG by logFC
... Hi, Can you post the code that you've used before and print the first few lines of your data? For instance I don't know how it looks your data, so I don't know that column names, and so on. I believe that you've used `DESeq2` for DEG, but it's not clear to me. António ...
written 2 days ago by antonioggsousa480
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Comment: C: Rarefaction of sequences before MetaPhlan analysis
... Yes, there isn't a consensus. This is one of these things that there is a lot of discussion and you probably will never find a consensus solution. I'm not familiar with MetaPhlAn, but I would say after the profiling step. I worked (and still work) with 16S rRNA gene amplicon data analysis and data ...
written 3 days ago by antonioggsousa480
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Comment: C: Rarefaction of sequences before MetaPhlan analysis
... Hi, According to one of the authors, yes you should rarefy to even sampling depth. Though there are other opinions on the field. Check the discussion here: https://groups.google.com/forum/#!topic/metaphlan-users/e2tets6NHK8 António ...
written 3 days ago by antonioggsousa480
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Comment: C: Getting mitochondrial genes for scRNAseq
... Yes. For instance one of the software used to analyze scRNA-seq data on R detects the percentage of mitochondrial genes by: pbmc[["percent.mt"]] <- PercentageFeatureSet(pbmc, pattern = "^MT-") As you can see on the option/parameter `pattern` the user needs to specify which is the pattern ...
written 3 days ago by antonioggsousa480
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Answer: A: Getting mitochondrial genes for scRNAseq
... Hi, The list of mitochondrial genes is obtained after align and annotate the reads of the scRNA-seq data. After this step you get a table usually with genes annotated on the rows and cells on the columns. Each gene contains a number of reads aligned against itself across each cell. Depending if ...
written 3 days ago by antonioggsousa480

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