User: A. Domingues
A. Domingues • 1.4k
- Reputation:
- 1,450
- Status:
- Trusted
- Location:
- Mainz, Germany
- Website:
- http://adomingues.gith...
- Twitter:
- keyboardpipette
- Last seen:
- 1 week, 2 days ago
- Joined:
- 5 years, 2 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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... `$fasta` is a variable that represents the input fasta. It should be defined before the loop as `fasta=my_fancy.fasta` ...
written 10 weeks ago by
A. Domingues • 1.4k
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... If I read the question correctly I think the OP is looking for something like piRNA clusters - regions enriched for certain types of smRNA. Slightlym different approach because the regions/clusters would have variable lengths, and most of the genome would be free of these. More like a aggregation op ...
written 4 months ago by
A. Domingues • 1.4k
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... I suggests a combination of `bedtools` [merge][1] or [cluster][2], depending on what is the final goal. For instance, using `merge`:
```
## code untested
bamToBed -i my.bam \ # converts bam to bed. Ensures that read ID is kept which will be useful for counting
| mergeBed -i stdin -c 4 -o count \ ...
written 4 months ago by
A. Domingues • 1.4k
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... Upvote for UpSetR. I used it recently, and though it took me some time to know how to read it properly - and explain it to my colleagues - it was easy enough to create a simple plot. Definitely and improvement on an 8-way venn which will be unreadable. ...
written 4 months ago by
A. Domingues • 1.4k
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... Using the [cgat toolset][1] it can be accomplished with:
```
cgat gtf2gtf --method=filter --filter-method=longest-transcript
```
It is a very rich set of tools, so have a look at what else it does because it will make your like easier.
[1]: https://www.cgat.org/downloads/public/cgat/documenta ...
written 4 months ago by
A. Domingues • 1.4k
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... *I hope this post doesn't come across too aggressive. As stated before I like and use both SE (mostly SO) and Biostars, and I am participating in the discussion because I feel that as good as Biostars is, it could be even better with a few minor changes.*
> Perhaps I am speculating on the motiv ...
written 4 months ago by
A. Domingues • 1.4k
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7
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3.1k
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7
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... > StackExchange has become envious of us - they want to heavily commercialize and push into the field of Bioinformatics
Is there evidence for this? ...
written 4 months ago by
A. Domingues • 1.4k
3
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7
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3.1k
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... Yes, and I suffered from that at the beginning, but I never had a post removed from SE. I got some slaps for poor questions and had to do some edits but otherwise fine. In the process I learned how to learn. This also means that I spend a lot of time looking for an answer before I post. Of course YM ...
written 5 months ago by
A. Domingues • 1.4k
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... Downvotes on SE also reduce the reputation points of the voter, so they can't exactly be handed out like candy. ...
written 5 months ago by
A. Domingues • 1.4k
7
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... > I hate SE as a medium, if you ask a simple question you get downvoted to oblivion and at best you get a condescending comment about your question without even an answer. It's a horrible teaching platform.
I disagree with this. I have used both Biostars **and** SE while learning and both helped ...
written 5 months ago by
A. Domingues • 1.4k
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12 weeks ago,
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For How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
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4 months ago,
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For A: MutSigCV output and coMut plots
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5 months ago,
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For C: how to parallelize single function in R?
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5 months ago,
created a comment with at least 3 up-votes.
For C: how to parallelize single function in R?
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For A: MutSigCV output and coMut plots
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For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
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For A: Bioinformatics Training On Next-Generation Sequencing Data
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6 months ago,
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For C: how to parallelize single function in R?
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For A: MutSigCV output and coMut plots
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For MutSigCV output and coMut plots
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10 months ago,
created a question with more than 1,000 views.
For problems with MAF for MutSigCV (vcf2maf)
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11 months ago,
created a question with more than 1,000 views.
For problems with MAF for MutSigCV (vcf2maf)
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: Bioinformatics Training On Next-Generation Sequencing Data
Teacher
11 months ago,
created an answer with at least 3 up-votes.
For A: Bioinformatics Training On Next-Generation Sequencing Data
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For Heatmap Of Read Coverage Around Tsss
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13 months ago,
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For problems with MAF for MutSigCV (vcf2maf)
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13 months ago,
created an answer with at least 3 up-votes.
For A: Bioinformatics Training On Next-Generation Sequencing Data
Scholar
16 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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