User: A. Domingues

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A. Domingues1.7k
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Location:
Mainz, Germany
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http://adomingues.gith...
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keyboardpipette
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an hour ago
Joined:
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

<prev • 215 results • page 1 of 22 • next >
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Comment: C: How to (and where) download Zebrafish Reference Genome (other than Ensembl or US
... 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. Domingues1.7k
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Answer: A: Normalization for small non-coding RNA (piRNAs)
... > 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. Domingues1.7k
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Answer: A: Normalization for small non-coding RNA (piRNAs)
... *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. Domingues1.7k
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Comment: C: Is Kallisto good for identifying non-coding RNA in a RNAseq data?
... 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. Domingues1.7k
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Comment: C: Normalization for small non-coding RNA (piRNAs)
... > 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. Domingues1.7k
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Answer: A: Normalization for small non-coding RNA (piRNAs)
... (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. Domingues1.7k
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Comment: C: Normalization for small non-coding RNA (piRNAs)
... 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. Domingues1.7k
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Answer: A: help identifying bioinformatics operations tools
... 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. Domingues1.7k
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Answer: A: smallRNA sequencing workflow and Database usage
... 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. Domingues1.7k
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Comment: C: Strategies for group submisions to SRA (BioProject)
... 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. Domingues1.7k

Latest awards to A. Domingues

Teacher 7 days ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Appreciated 14 days ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Great Question 5 weeks ago, created a question with more than 5,000 views. For Issue with naming convention in bedtools
Popular Question 10 weeks ago, created a question with more than 1,000 views. For rRNA quantification: which is the best way?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Great Question 11 weeks ago, created a question with more than 5,000 views. For problems with MAF for MutSigCV (vcf2maf)
Great Question 12 weeks ago, created a question with more than 5,000 views. For Heatmap Of Read Coverage Around Tsss
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Popular Question 6 months ago, created a question with more than 1,000 views. For rRNA quantification: which is the best way?
Popular Question 7 months ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals
Popular Question 8 months ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals
Student 10 months ago, asked a question with at least 3 up-votes. For Issue with naming convention in bedtools
Popular Question 10 months ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Popular Question 17 months ago, created a question with more than 1,000 views. For How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Appreciated 19 months ago, created a post with more than 5 votes. For A: from txt to bed
Good Answer 19 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 19 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Commentator 19 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 19 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Commentator 20 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?

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