Moderator: WouterDeCoster
WouterDeCoster ♦ 40k
- Reputation:
- 39,750
- Status:
- Trusted
- Location:
- Belgium
- Website:
- https://gigabaseorgiga...
- Twitter:
- wouter_decoster
- Last seen:
- an hour ago
- Joined:
- 3 years, 4 months ago
- Email:
- d*************@gmail.com
I am a research associate at the Center for Molecular Neurology, University of Antwerp & VIB, focussing on analysis of sequencing data with the aim of identifying variants relevant to neurodegenerative diseases, and mainly structural variants using long read PromethION sequencing.
Posts by WouterDeCoster
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... Your title says that you have a de novo assembled genome, but your question is about a species with (reference) genome, so what is it? ...
written 8 hours ago by
WouterDeCoster ♦ 40k
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... It's not a written rule. It's just etiquette. ...
written 21 hours ago by
WouterDeCoster ♦ 40k
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... Nobody has any obligation at all to keep on answering. ...
written 22 hours ago by
WouterDeCoster ♦ 40k
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... A good starting point would be [this workflow][1]. Feel free to open a new question if you have a more specific question afterward.
[1]: https://bioconductor.org/packages/devel/bioc/vignettes/tximport/inst/doc/tximport.html ...
written 1 day ago by
WouterDeCoster ♦ 40k
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Comment:
C: perseus expert assist
... How can we help you with your workflow if you don't show it? ...
written 1 day ago by
WouterDeCoster ♦ 40k
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... For your information, you can avoid intermediate files and save time by piping the output of bwa mem directly to samtools and create a sorted bam file:
bwa mem genome.fa reads.fastq.gz | samtools sort -o sorted_alignment.bam
This requires that your samtools is quite recent, but you should alwa ...
written 2 days ago by
WouterDeCoster ♦ 40k
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Comment:
C: VCF merge or concatenate?
... Not what you are asking for, but the currently recommended tool for things like this is `bcftools`, and no longer VCFtools. ...
written 2 days ago by
WouterDeCoster ♦ 40k
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... It may be obvious, but you used the same reference for your WGS and RNA-seq, right? Same chromosome names... ...
written 3 days ago by
WouterDeCoster ♦ 40k
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... > I am a beginner with Perl programming.
If you are now starting out with programming and can choose which language to learn, Perl is not the best choice. It was amazing for bioinformatics 10 years ago, but nowadays a better choice would be Python or R. ...
written 3 days ago by
WouterDeCoster ♦ 40k
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... > I have always used Samtools to remove any human contaminants from my gut flora data.
Well, samtools has multiple subcommands, and you can do a lot with it. It is probably most helpful if you describe more in detail what you did (which commands you used). ...
written 3 days ago by
WouterDeCoster ♦ 40k
Latest awards to WouterDeCoster
Good Answer
2 days ago,
created an answer that was upvoted at least 5 times.
For A: samtools sort bam file
Appreciated
21 days ago,
created a post with more than 5 votes.
For Workflow for structural variants from long read sequencing data
Good Answer
25 days ago,
created an answer that was upvoted at least 5 times.
For A: splitting a SAM file
Commentator
6 weeks ago,
created a comment with at least 3 up-votes.
For C: Bioinformatics freelancers needed
Appreciated
7 weeks ago,
created a post with more than 5 votes.
For Interesting bioinformatics blogs (2017 edition)
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: Most common practice for targeted sequencing analysis tools?
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For A: Most common practice for targeted sequencing analysis tools?
Teacher
8 weeks ago,
created an answer with at least 3 up-votes.
For A: Most common practice for targeted sequencing analysis tools?
Commentator
10 weeks ago,
created a comment with at least 3 up-votes.
For C: Fastest (non-pseudo) aligner for RNA-seq illumina seq data (year 2019)
Good Answer
10 weeks ago,
created an answer that was upvoted at least 5 times.
For A: splitting a SAM file
Appreciated
10 weeks ago,
created a post with more than 5 votes.
For A: Is there any way to install RStudio (or any other powerful IDE for R) without ro
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