User: A. Domingues
A. Domingues • 1.8k
- Reputation:
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- Location:
- Mainz, Germany
- Website:
- http://adomingues.gith...
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- keyboardpipette
- Last seen:
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- Joined:
- 6 years, 7 months ago
- Email:
- a***********@gmail.com
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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... We have a mutant (gene KO) that displays two different phenotypes identified by the presence or absence of expression of a reporter. Since this mutation is in gene that is part of an endogenous RNAi pathway, and the strains have the same genotype, we hypothesized that the report status is not due to ...
written 24 days ago by
A. Domingues • 1.8k
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... > The only worry I've had in the past with ATAC-seq data is comparison between samples with drastically different chromatin states.
@James Ashmore I currently running into the same situation as described above. Have you seed a reasonable solution to compare these type of samples? I have been sug ...
written 5 weeks ago by
A. Domingues • 1.8k
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... Another reason why using databases of piRNAs might not be a great idea:
> Non-coding RNA fragments account for the majority of annotated piRNAs expressed in somatic non-gonadal tissues.
> https://www.ncbi.nlm.nih.gov/pubmed/30271890
...
written 6 weeks ago by
A. Domingues • 1.8k
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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 10 weeks ago by
A. Domingues • 1.8k
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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 10 weeks ago by
A. Domingues • 1.8k
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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 10 weeks ago by
A. Domingues • 1.8k
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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 10 weeks ago by
A. Domingues • 1.8k
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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 10 weeks ago by
A. Domingues • 1.8k
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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 11 weeks ago by
A. Domingues • 1.8k
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... What is the biological question, or comparison, you are interested in? Are there other conditions besides control vs treatment? ...
written 11 weeks ago by
A. Domingues • 1.8k
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For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
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10 weeks ago,
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For A: Bioinformatics Training On Next-Generation Sequencing Data
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For A: MutSigCV output and coMut plots
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3 months ago,
created an answer that has been accepted.
For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
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For Issue with naming convention in bedtools
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For rRNA quantification: which is the best way?
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4 months ago,
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For A: Bioinformatics Training On Next-Generation Sequencing Data
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For problems with MAF for MutSigCV (vcf2maf)
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For Heatmap Of Read Coverage Around Tsss
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For A: MutSigCV output and coMut plots
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9 months ago,
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For rRNA quantification: which is the best way?
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For How to identify consecutive (adjacent) genomic intervals
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For How to identify consecutive (adjacent) genomic intervals
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12 months ago,
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For Issue with naming convention in bedtools
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12 months ago,
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For How to identify consecutive (adjacent) genomic intervals
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15 months ago,
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For A: Bioinformatics Training On Next-Generation Sequencing Data
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20 months ago,
created a question with more than 1,000 views.
For How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
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21 months ago,
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For C: how to parallelize single function in R?
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For C: how to parallelize single function in R?
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22 months ago,
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For C: how to parallelize single function in R?
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