User: A. Domingues
A. Domingues • 1.7k
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- Mainz, Germany
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- http://adomingues.gith...
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- keyboardpipette
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- 6 years, 5 months ago
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Biologist doing research in gene expression regulation with a background in neurobiology and entering the world of bioinformatics.
Posts by A. Domingues
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... This is *usually* good advice, but as of today, `GRCz11/danRer11` is not available as a bundle, so it doesn't help the OP. ...
written 2 days ago by
A. Domingues • 1.7k
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... > rRNA, miRNA, tRNA
I forgot to add that based simply on mapping to these annotated features, it is quite likely the reads are not originating from piRNAs. ...
written 7 days ago by
A. Domingues • 1.7k
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... *edit: this should have been a comment. It's late.*
> But how do we now that these kinds of reads derive from piRNAs?
I would thread carefully in the case of piRNA derived from protein-coding genes. But you can still, and very naively count reads mapping to annotated genomic features such as ...
written 7 days ago by
A. Domingues • 1.7k
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... Adding to what WouterDeCoster said: (i) a lot of non-coding RNAs are relatively small, which means that depending on which sequencing protocol was they might not have been sequenced at all; (ii) they might also be repetitive leading to multimapping reads which I am not sure Kallisto would be able to ...
written 7 days ago by
A. Domingues • 1.7k
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... > I align reads with length>15.
This is very short. I would start at about 18 bp and even then I can't of a small RNA that small (though they might exist).
> I thought that there is a difference between a multi-mapping read and a multi-mapped small-RNA(piRNA) but when we have that kind of ...
written 8 days ago by
A. Domingues • 1.7k
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... (this is a bit too long for a comment so adding it as an answer)
Judging also from your post in [BioC](https://support.bioconductor.org/p/115459/#115539) it seems like you are interested in a sort non-standard analysis, or at least one that I am not familiar with. First things first.
> Are piRN ...
written 9 days ago by
A. Domingues • 1.7k
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... What is the biological question, or comparison, you are interested in? Are there other conditions besides control vs treatment? ...
written 15 days ago by
A. Domingues • 1.7k
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... Miso-lims seems to be appropriate for your tasks:
> Hence, we are developing MISO, an open-source LIMS for recording sequencing metadata. We are using freely available tools that are industry standard, well documented, and easy to set up on minimal hardware. As a bare system, MISO can store rele ...
written 21 days ago by
A. Domingues • 1.7k
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... Welcome to the wonderfully strange world of piRNAs :) I will first urge to read two of my previous answers on the subject:
https://www.biostars.org/p/235278/#235289
https://www.biostars.org/p/179944/#228109
TLDR; if you are novice, use piPipes. Very easy to set-up, specially if you are working wit ...
written 4 weeks ago by
A. Domingues • 1.7k
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... Yes, I have been there. Looking for total (rRNA-depleted) RNA-seq datasets was a nightmare a few years ago. I might be wrong, but it also looks like the submission forms have improved over the years and now there many, and very specific, options for library type for example. ...
written 7 weeks ago by
A. Domingues • 1.7k
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