Moderator: WouterDeCoster

gravatar for WouterDeCoster
Reputation:
13,180
Status:
Trusted
Location:
Belgium
Twitter:
wouter_decoster
Last seen:
2 hours ago
Joined:
11 months, 2 weeks ago
Email:
d*************@gmail.com

I'm a PhD student at the University of Antwerp (VIB department of Molecular Genetics) 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 • 2,723 results • page 1 of 273 • next >
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Comment: C: kmergenie Installation failed. seems got a bug
... I think 'kmergenie' would be a logical tag for this post, I added this. If you need support of the authors, best to use tags. ...
written 5 hours ago by WouterDeCoster13k
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Comment: C: SNPs Calling Tools
... Tools like GATK will perform sub-optimal on PacBio data since GATK is mainly designed for Illumina data. You can use them, but more specific variant callers would do better. However, I'm not aware of PacBio-specific variant callers, perhaps this page can put you in the right direction: http://www.pa ...
written 8 hours ago by WouterDeCoster13k
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Comment: C: What second field zero means in sam file?
... The read is not paired, not unmapped and not on the reverse strand. Therefore the reads is from a SE experiment, therefore the read is mapped, therefore the read is on the + strand. ...
written 9 hours ago by WouterDeCoster13k
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Comment: C: Best visual and interactive genotype matrix (VCF) exploration tool
... I was a bit confused what the 'main screen' "set location of all frames to" option would do, having been too quick in the manual. In hindsight it's clear, but I wouldn't have wondered about it if the text would have been something like "change genomic location of all frames to", with maybe an exampl ...
written 9 hours ago by WouterDeCoster13k
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Comment: C: Best visual and interactive genotype matrix (VCF) exploration tool
... Right, that did the trick ;-) I'm going to play a bit with it, for sure looks great. Thanks! ...
written 10 hours ago by WouterDeCoster13k
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Comment: C: Best visual and interactive genotype matrix (VCF) exploration tool
... I tried installing on Ubuntu 16.04, and get `home/wouter/bin/jvarkit/src/main/java/com/github/lindenb/jvarkit/tools/vcfviewgui/VcfStage.java:74: error: package javafx.beans.property does not exist`, followed by many more of similar errors each pointing to a different package that doesn't exist. Bef ...
written 1 day ago by WouterDeCoster13k
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Comment: C: IGV white read color meaning
... As far as I know those colours can be adjusted by the users, but I think the default for white/light grey is mapping quality of 0. You could check this easily by checking the mapping quality of the white reads... ...
written 1 day ago by WouterDeCoster13k
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Comment: C: PCA of Cuffdiff output
... I doubt if doing PCA on 6 samples will give you enough information to reliably identify batch effects. Did you use bowtie for alignment? Because that's not an appropriate for human RNA-seq. ...
written 1 day ago by WouterDeCoster13k
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Comment: C: GC Content of Fasta file --- Python Help
... Biopython SeqIO can spare you many headaches when parsing common filetypes, including fasta. See the excellent [tutorial and cookbook][1]. My code below also uses SeqIO My code boils down to following core functions: def getGC(seq): return(str(int(round((sum([1.0 for nucl in seq if nucl i ...
written 1 day ago by WouterDeCoster13k
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Comment: C: error in bowtie 2
... Please use `ADD REPLY` to answer to earlier comments, as such this thread remains logically structured and easy to follow. For RNA-seq alignment of eukaryotic genomes you need a spliced aligner, most recommended nowadays are STAR and HISAT2. ...
written 1 day ago by WouterDeCoster13k

Latest awards to WouterDeCoster

Scholar 6 hours ago, created an answer that has been accepted. For A: how can I obtain benign / neutral snps?
Scholar 2 days ago, created an answer that has been accepted. For A: how can I obtain benign / neutral snps?
Commentator 3 days ago, created a comment with at least 3 up-votes. For C: Bioinformatics freelancers needed
Commentator 11 days ago, created a comment with at least 3 up-votes. For C: Bioinformatics freelancers needed
Commentator 11 days ago, created a comment with at least 3 up-votes. For C: Bioinformatics freelancers needed
Commentator 11 days ago, created a comment with at least 3 up-votes. For C: Bioinformatics freelancers needed
Teacher 12 days ago, created an answer with at least 3 up-votes. For A: What does + stand for in sequence alignment (blastp)?
Scholar 13 days ago, created an answer that has been accepted. For A: how can I obtain benign / neutral snps?
Teacher 13 days ago, created an answer with at least 3 up-votes. For A: What does + stand for in sequence alignment (blastp)?
Commentator 18 days ago, created a comment with at least 3 up-votes. For C: Bioinformatics freelancers needed
Scholar 18 days ago, created an answer that has been accepted. For A: how can I obtain benign / neutral snps?
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: What does + stand for in sequence alignment (blastp)?
Scholar 22 days ago, created an answer that has been accepted. For A: how can I obtain benign / neutral snps?
Scholar 22 days ago, created an answer that has been accepted. For A: How to do gene enrichment analysis?
Commentator 23 days ago, created a comment with at least 3 up-votes. For C: Bioinformatics freelancers needed
Commentator 24 days ago, created a comment with at least 3 up-votes. For C: Bioinformatics freelancers needed
Teacher 25 days ago, created an answer with at least 3 up-votes. For A: What does + stand for in sequence alignment (blastp)?
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 can I obtain benign / neutral snps?
Commentator 5 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 can I obtain benign / neutral snps?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: What does + stand for in sequence alignment (blastp)?
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: What does + stand for in sequence alignment (blastp)?
Scholar 7 weeks ago, created an answer that has been accepted. For A: how can I obtain benign / neutral snps?

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