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Recent Replies
Answer: metagenomic virome quality assessment
by
Mensur Dlakic
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The error message points to a problem with `prodigal-gv`. What happens when you type `prodigal-gv` on the command line?
It is never a go…
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"I have seen other similar posts but a lot of the tools and websites suggested are down."
Please show & share your research as part of you…
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No... the extracted sample is already a mix so no way to barcode
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For anyone it might be useful: a colleague of mine, who was not dumb to use the wrong annotation `gtf`, also observed an important issue of…
Answer: Very low RNA splicing rate for pulmonary AT2 cells
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e.r.zakiev
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Hello people sorry I am dumb the problem lied in the fact that I had mouse cells but my `.gtf` transcriptome file was for the human. Now wi…
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Can you indicate if you need to do this within CLC or can use an external solution (if someone provides it here). If you need to do this in…
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The file being PE should not matter. I'd recommend you open an issue on the seqtk github repo as this is starting to look like some sort of…
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Do the developers of toil mention biostars? Where do they direct their support requests to?
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dsull
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As an additional note, all those ``--include-attribute`` stuff was basically to restrict the transcriptome to precisely the items that Cell…
Answer: How should I make kallisto indexes?
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I recommend the ``kb ref`` method for two reasons:
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Were these samples barcoded when they were run. If not then you won't be able to do much.
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The approach you are using here is the old method. Seurat is updated to V5. Please try Seurat V5 integrative analysis described in the link…
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Hi, you can still use `kallisto index -i transcripts.index transcripts.fa` (extract the gz file) for making index files. I have tried it an…
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Thanks for the suggestion, but I get several lines of results (see below) and although there are directories called `"R"`, I can't find any…
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Malat1 is a lncRNA abundant in the nucleus. I guess if Malat1 is abundant and stable, makes sense it could be detect in high amounts in scR…
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