User: A. Domingues

gravatar for A. Domingues
A. Domingues1.4k
Reputation:
1,450
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Location:
Mainz, Germany
Website:
http://adomingues.gith...
Twitter:
keyboardpipette
Last seen:
15 hours ago
Joined:
5 years 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

<prev • 193 results • page 1 of 20 • next >
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Comment: C: Filtering Fasta Sequences By Chromosomes Names From A Big Fasta File
... `$fasta` is a variable that represents the input fasta. It should be defined before the loop as `fasta=my_fancy.fasta` ...
written 14 days ago by A. Domingues1.4k
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Comment: C: small RNA-seq reads grouping by adjacency
... 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 11 weeks ago by A. Domingues1.4k
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Answer: A: small RNA-seq reads grouping by adjacency
... 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 11 weeks ago by A. Domingues1.4k
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Comment: C: Venn diagrams for multiple (8) data lists in R
... 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 11 weeks ago by A. Domingues1.4k
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Answer: A: how to select longest isoform per gene in gtf
... 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 11 weeks ago by A. Domingues1.4k
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Comment: C: StackExchange/Area51 bioinformatics is back
... *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 11 weeks ago by A. Domingues1.4k
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Comment: C: StackExchange/Area51 bioinformatics is back
... > StackExchange has become envious of us - they want to heavily commercialize and push into the field of Bioinformatics Is there evidence for this? ...
written 11 weeks ago by A. Domingues1.4k
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Comment: C: StackExchange/Area51 bioinformatics is back
... 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 3 months ago by A. Domingues1.4k
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Comment: C: StackExchange/Area51 bioinformatics is back
... Downvotes on SE also reduce the reputation points of the voter, so they can't exactly be handed out like candy. ...
written 3 months ago by A. Domingues1.4k
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Comment: C: StackExchange/Area51 bioinformatics is back
... > 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 3 months ago by A. Domingues1.4k

Latest awards to A. Domingues

Popular Question 29 days ago, created a question with more than 1,000 views. For How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: from txt to bed
Good Answer 9 weeks ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 11 weeks ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Commentator 11 weeks ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 12 weeks ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Commentator 3 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 4 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Scholar 4 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Appreciated 6 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Student 6 months ago, asked a question with at least 3 up-votes. For MutSigCV output and coMut plots
Popular Question 7 months ago, created a question with more than 1,000 views. For problems with MAF for MutSigCV (vcf2maf)
Guru 8 months ago, received more than 100 upvotes.
Popular Question 8 months ago, created a question with more than 1,000 views. For problems with MAF for MutSigCV (vcf2maf)
Popular Question 9 months ago, created a question with more than 1,000 views. For problems with MAF for MutSigCV (vcf2maf)
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Teacher 9 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Great Question 10 months ago, created a question with more than 5,000 views. For Heatmap Of Read Coverage Around Tsss
Popular Question 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
Scholar 14 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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