User: A. Domingues

gravatar for A. Domingues
A. Domingues2.1k
Reputation:
2,090
Status:
Trusted
Location:
Dresden, Germany
Website:
http://adomingues.gith...
Twitter:
keyboardpipette
Last seen:
14 hours ago
Joined:
7 years, 3 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

<prev • 231 results • page 1 of 24 • next >
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Comment: C: How to use RIPSeeker?
... No modification at all, I simply did a IP / input comparison and it worked well - at least that is what my colleagues which did the experimental validation told me. ...
written 10 days ago by A. Domingues2.1k
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Comment: C: How to use RIPSeeker?
... Not an answer but unless you really need to use RIPseeker, I would advise to look for alternatives. As far as I can tell development as been stagnating fro a long time now, with the last commit in github being 2 years ago, and pull requests and issues going unanswered from around that time. I also r ...
written 12 days ago by A. Domingues2.1k
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Comment: C: Expression of transposons in transcriptomes
... No idea. I suggest asking the developers in github. They have been quite responsive whenever I had similar questions. ...
written 3 months ago by A. Domingues2.1k
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Answer: A: Expression of transposons in transcriptomes
... I have used [SalmonTE](https://github.com/LiuzLab/SalmonTE) in the past and had good experiences. It uses `salmon` the background but then aggregates the counts per element, family and class. The results tables are also ready to use with `DESeq2` ...
written 3 months ago by A. Domingues2.1k
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Comment: C: Middle author, but not first author projects. How would you approach this?
... 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 6 months ago by A. Domingues2.1k
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Comment: C: Middle author, but not first author projects. How would you approach this?
... > 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 6 months ago by A. Domingues2.1k
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Comment: C: Middle author, but not first author projects. How would you approach this?
... 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 6 months ago by A. Domingues2.1k
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Answer: A: Middle author, but not first author projects. How would you approach this?
... 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 6 months ago by A. Domingues2.1k
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Comment: C: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
... Alicia Oshlack in particular has been doing a lot of good stuff under the radar: bpipe, diffvar, missMethyl,and clustree. ...
written 6 months ago by A. Domingues2.1k
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Answer: A: HTSeq errors in the command line
... 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 7 months ago by A. Domingues2.1k

Latest awards to A. Domingues

Popular Question 7 weeks ago, created a question with more than 1,000 views. For Project organization: make code public and keep notes private
Popular Question 3 months ago, created a question with more than 1,000 views. For Project organization: make code public and keep notes private
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Commentator 6 months ago, created a comment with at least 3 up-votes. For C: how to parallelize single function in R?
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Appreciated 6 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Good Answer 6 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Scholar 10 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Appreciated 10 months ago, created a post with more than 5 votes. For A: MutSigCV output and coMut plots
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Scholar 11 months ago, created an answer that has been accepted. For A: How to had CDS feature with cufflinks (cuffmerge) using custom GTF?
Great Question 11 months ago, created a question with more than 5,000 views. For Issue with naming convention in bedtools
Popular Question 12 months ago, created a question with more than 1,000 views. For rRNA quantification: which is the best way?
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Bioinformatics Training On Next-Generation Sequencing Data
Great Question 12 months ago, created a question with more than 5,000 views. For problems with MAF for MutSigCV (vcf2maf)
Great Question 13 months ago, created a question with more than 5,000 views. For Heatmap Of Read Coverage Around Tsss
Good Answer 14 months ago, created an answer that was upvoted at least 5 times. For A: MutSigCV output and coMut plots
Popular Question 17 months ago, created a question with more than 1,000 views. For rRNA quantification: which is the best way?
Popular Question 17 months ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals
Popular Question 19 months ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals
Student 20 months ago, asked a question with at least 3 up-votes. For Issue with naming convention in bedtools
Popular Question 20 months ago, created a question with more than 1,000 views. For How to identify consecutive (adjacent) genomic intervals

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