User: A. Domingues

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A. Domingues1.8k
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Location:
Mainz, Germany
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http://adomingues.gith...
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keyboardpipette
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2 hours ago
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6 years, 7 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 • 218 results • page 1 of 22 • next >
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How to test gene expression variability - expression differences independent of genotype
... 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 ...
gene expression deseq2 rna-seq written 24 days ago by A. Domingues1.8k
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Comment: C: Does read counts for ATAC-seq differential detection make sense?
... > 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. Domingues1.8k
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Comment: C: smallRNA sequencing workflow and Database usage
... 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. Domingues1.8k
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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 10 weeks ago by A. Domingues1.8k
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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 10 weeks ago by A. Domingues1.8k
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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 10 weeks ago by A. Domingues1.8k
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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 10 weeks ago by A. Domingues1.8k
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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 10 weeks ago by A. Domingues1.8k
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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 11 weeks ago by A. Domingues1.8k
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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 11 weeks ago by A. Domingues1.8k

Latest awards to A. Domingues

Scholar 9 weeks ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Scholar 3 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Great Question 3 months ago, created a question with more than 5,000 views. For Issue with naming convention in bedtools
Popular Question 4 months ago, created a question with more than 1,000 views. For rRNA quantification: which is the best way?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Great Question 5 months ago, created a question with more than 5,000 views. For problems with MAF for MutSigCV (vcf2maf)
Great Question 5 months ago, created a question with more than 5,000 views. For Heatmap Of Read Coverage Around Tsss
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Popular Question 9 months ago, created a question with more than 1,000 views. For rRNA quantification: which is the best way?
Popular Question 9 months ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals
Popular Question 11 months ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals
Student 12 months ago, asked a question with at least 3 up-votes. For Issue with naming convention in bedtools
Popular Question 12 months ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals
Teacher 15 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Popular Question 20 months ago, created a question with more than 1,000 views. For How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Appreciated 21 months ago, created a post with more than 5 votes. For A: from txt to bed
Good Answer 21 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Commentator 21 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 21 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
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Appreciated 22 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Commentator 22 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?

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