Moderator: WouterDeCoster
WouterDeCoster ♦ 42k
- Reputation:
- 41,710
- Status:
- Trusted
- Location:
- Belgium
- Website:
- https://gigabaseorgiga...
- Twitter:
- wouter_decoster
- Last seen:
- 36 minutes ago
- Joined:
- 3 years, 8 months ago
- Email:
- d*************@gmail.com
I am a postdoctoral researcher and research associate at the Center for Molecular Neurology, University of Antwerp & VIB, focussing on the 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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Comment:
C: RPKM with bowtie output
... > The script is throwing errors.
How do you expect us to help if you don't tell us what's going wrong? ...
written 6 hours ago by
WouterDeCoster ♦ 42k
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... Why do you tag this as "assembly" while you are aligning? Why do you think this is a "software error"? Wouldn't "minimap2" be the best tag here? ...
written 6 hours ago by
WouterDeCoster ♦ 42k
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... You could consider avoiding creating a sam intermediate:
minimap2 -a -t 20 reference.mmi query.fasta | samtools sort -o output.bam
...
written 7 hours ago by
WouterDeCoster ♦ 42k
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... > Where does Targeted Panel sequencing come in terms of library preparation in sequencing
What does that question mean? ...
written 8 hours ago by
WouterDeCoster ♦ 42k
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... use [samtools faidx][1] to index and retrieve those coordinates
[1]: http://www.htslib.org/doc/samtools.html ...
written 8 hours ago by
WouterDeCoster ♦ 42k
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... Oh yes, if you already know what you are looking for then a targeted panel is fine. ...
written 8 hours ago by
WouterDeCoster ♦ 42k
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... You are confused. You claim WES/panel is better than WGS here, while the difference is just the sequencing depth. If you do ultra-deep WGS you would find the same (and much more!). It's not a matter of technology, but of depth. ...
written 9 hours ago by
WouterDeCoster ♦ 42k
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Comment:
C: MUMmer . Global alignment
... > i was trying to do Global alignment using nucmer package
Please be more specific about what you are doing and why, what your data is and what you aim to achieve.
> but i didn't undrestand results
Please be more specific about the results you got and how that was unclear.
> can anyone ...
written 9 hours ago by
WouterDeCoster ♦ 42k
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... > if genomic DNA is extracted from tissues, and the goal is to find variants such as SNP, indels, CNVs-which is the preferred method- whole exome sequencing or whole genome sequencing and why?
SNPs and short indels can be called both using WES and WGS. However, you can only call variants if they ...
written 10 hours ago by
WouterDeCoster ♦ 42k
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... > I tried few packages in R but no luck
Please show us what you have tried ...
written 22 hours ago by
WouterDeCoster ♦ 42k
Latest awards to WouterDeCoster
Teacher
9 hours ago,
created an answer with at least 3 up-votes.
For A: Merging multiple vcfs with GATK's CombineVariants
Appreciated
10 days ago,
created a post with more than 5 votes.
For A: Merging multiple vcfs with GATK's CombineVariants
Good Answer
11 days ago,
created an answer that was upvoted at least 5 times.
For A: Merging multiple vcfs with GATK's CombineVariants
Teacher
13 days ago,
created an answer with at least 3 up-votes.
For C: Doing differential gene expression without knowing sample classes
Good Answer
19 days ago,
created an answer that was upvoted at least 5 times.
For A: samtools sort bam file
Appreciated
19 days ago,
created a post with more than 5 votes.
For A: How to use htseq-count with several samples ?
Teacher
19 days ago,
created an answer with at least 3 up-votes.
For C: Doing differential gene expression without knowing sample classes
Teacher
19 days ago,
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For C: Doing differential gene expression without knowing sample classes
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5 weeks ago,
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For C: Bioinformatics freelancers needed
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7 weeks ago,
created an answer with at least 3 up-votes.
For C: Doing differential gene expression without knowing sample classes
Teacher
7 weeks ago,
created an answer with at least 3 up-votes.
For C: Doing differential gene expression without knowing sample classes
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8 weeks ago,
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For C: Bioinformatics freelancers needed
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8 weeks ago,
created an answer with at least 3 up-votes.
For C: Doing differential gene expression without knowing sample classes
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For C: Bioinformatics freelancers needed
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For C: is fortran still used in bioinformatics?
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For C: Doing differential gene expression without knowing sample classes
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10 weeks ago,
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For C: Doing differential gene expression without knowing sample classes
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