Moderator: WouterDeCoster

gravatar for WouterDeCoster
Reputation:
23,820
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Location:
Belgium
Website:
https://gigabaseorgiga...
Twitter:
wouter_decoster
Last seen:
an hour ago
Joined:
1 year, 9 months ago
Email:
d*************@gmail.com

I'm a PhD student at the University of Antwerp (VIB Center for Molecular Neurology) with a background in biochemistry. I mainly work on data generated by genome sequencing, exome sequencing, targeted resequencing, RNA-seq and Nanopore Sequencing using MinION.

Posts by WouterDeCoster

<prev • 4,695 results • page 1 of 470 • next >
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Comment: C: HTSeq special counters occur at top and bottom of output file
... That will print the output to the terminal right? You miss the part where you redirect the output to a file. ...
written 1 hour ago by WouterDeCoster24k
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Comment: C: How to determine parent of origin of phased variants when all members are het
... > phasing software that uses inheritance information That's new information, you didn't specify this before. It should be feasible to identify the parent for each block if those are sufficiently big. You just have to find variant(s) specific to one parent to assign the entire block. ...
written 1 hour ago by WouterDeCoster24k
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Comment: C: HTSeq special counters occur at top and bottom of output file
... Please add the commands you used to obtain this result. ...
written 1 hour ago by WouterDeCoster24k
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Answer: A: How to determine parent of origin of phased variants when all members are het
... > I believe it's Haplotype Block A | Haplotype Block B. Indeed. Wherever possible using read-based evidence variants are phased in blocks, but e.g. across the repetitive elements, this information is lost. So this does not correspond to maternal and paternal haplotypes and needs long distance ph ...
written 1 hour ago by WouterDeCoster24k
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Comment: C: Opinion on Quality basecall threshold to use
... The variant call is a combination of the basecall, the coverage, the strand bias, the sequence context, the cycle number,... among other things, which all add evidence to the variant as being true. Essentially, all metrics the variant caller software uses to determine if this position has a variant ...
written 1 hour ago by WouterDeCoster24k
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Comment: C: Merge fastq reads for several samples
... You'll need a for loop for this, and to figure out how to write this command we need to know how your files are named, which naming pattern you use to distinguish the samples/lanes/read direction. ...
written 4 hours ago by WouterDeCoster24k
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Comment: C: Paired-end SRA data comes out as a Single-end
... `SRR87406` is not part of this dataset. Did you mean SRR870466? ...
written 15 hours ago by WouterDeCoster24k
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Comment: C: Subtracting one FASTAq file Reads from other FASTAq reads
... You probably mean a fastq file, since a 'fastaq' file does as far as I know not exist. ...
written 16 hours ago by WouterDeCoster24k
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Comment: C: Opinion on Quality basecall threshold to use
... That's the quality of the variant call, not of the basecall. The basecall quality is in the fastq files. ...
written 16 hours ago by WouterDeCoster24k
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Comment: C: How to simulate RNA-seq raw read counts matrix
... Might make more sense to close the other thread, this question makes more sense imho. ...
written 2 days ago by WouterDeCoster24k

Latest awards to WouterDeCoster

Scholar 1 hour ago, created an answer that has been accepted. For A: How to determine parent of origin of phased variants when all members are het
Commentator 12 days ago, created a comment with at least 3 up-votes. For C: Bioinformatics freelancers needed
Scholar 13 days ago, created an answer that has been accepted. For A: How to add single gene name in volcano plot ?
Commentator 19 days ago, created a comment with at least 3 up-votes. For C: Bioinformatics freelancers needed
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Scholar 4 weeks ago, created an answer that has been accepted. For A: How to add single gene name in volcano plot ?
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Bioinformatics freelancers needed
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to add single gene name in volcano plot ?
Good Answer 4 weeks ago, created an answer that was upvoted at least 5 times. For A: Stranger Things: unexpected limitations of popular tools
Appreciated 4 weeks ago, created a post with more than 5 votes. For Interesting bioinformatics blogs (2017 edition)
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: What exactly is sequencing depth in RNAseq?
Scholar 4 weeks ago, created an answer that has been accepted. For A: How to add single gene name in volcano plot ?
Commentator 4 weeks ago, created a comment with at least 3 up-votes. For C: Bioinformatics freelancers needed
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to add single gene name in volcano plot ?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: What exactly is sequencing depth in RNAseq?
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to add single gene name in volcano plot ?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: What exactly is sequencing depth in RNAseq?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Stranger Things: unexpected limitations of popular tools
Scholar 5 weeks ago, created an answer that has been accepted. For A: How to add single gene name in volcano plot ?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Stranger Things: unexpected limitations of popular tools
Good Answer 6 weeks ago, created an answer that was upvoted at least 5 times. For A: Stranger Things: unexpected limitations of popular tools
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Stranger Things: unexpected limitations of popular tools
Scholar 6 weeks ago, created an answer that has been accepted. For A: How to add single gene name in volcano plot ?
Commentator 6 weeks ago, created a comment with at least 3 up-votes. For C: Bioinformatics freelancers needed

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