User: A. Domingues
A. Domingues • 2.1k
- Reputation:
- 2,060
- Status:
- Trusted
- Location:
- Mainz, Germany
- Website:
- http://adomingues.gith...
- Twitter:
- keyboardpipette
- Last seen:
- 13 hours ago
- Joined:
- 6 years, 11 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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... This. It's a huge change in contractual terms. Had it been suggested to me I would have flat out refused it. If insisted upon I would start applying to other positions. ...
written 10 weeks ago by
A. Domingues • 2.1k
2
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5
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... > I was considering a staff scientist career, but I wouldn’t like to do it with postdoctoral contracts.
And rightly so. Since your background is mathematics, you might need to be on a postdoctoral contract for a period of time to show that you can hack it in a biology setting (communication can ...
written 10 weeks ago by
A. Domingues • 2.1k
3
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5
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1.4k
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... I second this. Our lab values computational work so that works for me, but I am sure not all groups do. This needs to be seriously discussed. There are more jobs out there. ...
written 10 weeks ago by
A. Domingues • 2.1k
11
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... Fellow "pet bioinformatician" here. I am also an a Postdoc but that is just the title of the position. In practice, and it was the agreement from the beginning, I am more of a staff bioinformatician which handles all of the (NGS/genomics) data analysis needs of the lab. I could have started my own i ...
written 11 weeks ago by
A. Domingues • 2.1k
2
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14
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2.0k
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14
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... Alicia Oshlack in particular has been doing a lot of good stuff under the radar: bpipe, diffvar, missMethyl,and clustree. ...
written 11 weeks ago by
A. Domingues • 2.1k
0
votes
1
answer
288
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1
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... You are directing your output to a directory. Try this:
```bash
htseq-count -f bam -q -m union -s yes -t exon -i gene_id ~/RNAseq/mapping/star/Treated_1.bam Treated_2.bam Untreated_1.bam Untreated_2.bam ~/RNAseq/annotation/Homo_sapiens.GRCh37.75.gtf > /home/RNAseq/htseq-count/countReads/all.cou ...
written 3 months ago by
A. Domingues • 2.1k
2
votes
2
answers
3.3k
views
2
answers
... I believe you could also use [seqtk][1] to do this:
`seqtk seq -L 25 yourseqs.fastq.gz > cleanseqs.fastq.gz `
[1]: https://github.com/lh3/seqtk/ ...
written 3 months ago by
A. Domingues • 2.1k
2
votes
1
answer
196
views
1
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... **Short answer**
Probably not.
**Long answer**
You will need to check with whomever prepared the libraries, but judging from the description alone
> I have a paired-end, stranded RNA dataset sequenced with Illumina TruSeq
I would say it is highly unlikely that there are any small RNAs there ...
written 4 months ago by
A. Domingues • 2.1k
0
votes
5
answers
9.3k
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5
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... Hi Giovanni, how did you end up solving this? I ran into a very similar [problem](https://www.biostars.org/p/360444/). ...
written 4 months ago by
A. Domingues • 2.1k
0
votes
0
answers
228
views
0
answers
... 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 5 months ago by
A. Domingues • 2.1k
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For A: Bioinformatics Training On Next-Generation Sequencing Data
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10 weeks ago,
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For C: how to parallelize single function in R?
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10 weeks ago,
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For C: how to parallelize single function in R?
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11 weeks ago,
created a post with more than 5 votes.
For A: MutSigCV output and coMut plots
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created an answer that was upvoted at least 5 times.
For A: MutSigCV output and coMut plots
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11 weeks ago,
created an answer with at least 3 up-votes.
For A: Bioinformatics Training On Next-Generation Sequencing Data
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3 months ago,
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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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6 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 A: MutSigCV output and coMut plots
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7 months ago,
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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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For Issue with naming convention in bedtools
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10 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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For Issue with naming convention in bedtools
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For How to identify consecutive (adjacent) genomic intervals
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For A: Bioinformatics Training On Next-Generation Sequencing Data
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For How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
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