Moderator: WouterDeCoster

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wouter_decoster
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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

<prev • 7,429 results • page 1 of 743 • next >
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Comment: C: methplotlib: visualization and analysis of modified nucleotides from nanopore se
... It's perhaps easy to remember, and as a scientist, you can't be a bit "creative" that often... :) ...
written 5 hours ago by WouterDeCoster43k
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Tool: methplotlib: visualization and analysis of modified nucleotides from nanopore sequencing
... We recently published [methplotlib][1], a tool for the visualization and analysis of modified nucleotides from nanopore sequencing. It works downstream of tools like [nanopolish][2], [nanocompore][3] and direct methylation calling by the guppy basecaller. More information can be found on [GitHub][4] ...
methylation tool nanopore sequencing written 21 hours ago by WouterDeCoster43k
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Answer: A: Ru/Read Until in Nanopore sequencers
... You are absolutely right, this is indeed a game-changer. However, there are some considerations to make. If you have a very small target out of a larger genome, you are effectively rejecting >99.9% of your reads, which will be rather bad for your yield. As mentioned in the preprint the yield is l ...
written 1 day ago by WouterDeCoster43k
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Comment: C: Loss of reads during realignment bam
... To convert a hg19 bam to hg38 you would indeed use bazam. To align reads in fastq format to GRCh38 you would use bwa mem. I believe bazam uses bwa mem under the hood, and handles the correct conversion to fastq so you don't have to worry about those steps. ...
written 5 days ago by WouterDeCoster43k
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Answer: A: Nanopolish variant calling. Need to specify input region of the reference genome
... Chromosomes are irrelevant. The tool looks at contigs regardless of how well assembled these are, and considers every sequence in your reference fasta a contig. Say that you have the following fasta file: >my_fabulous_contig ATGCGCGCGC >and_another_contig GCTTACTTGTG ...
written 6 days ago by WouterDeCoster43k
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Comment: C: Vegetable databases usage
... You should add a lot more information here, because your question is wildly unclear. > However, in some cases we have meat mixed with vegetables and want only to detect the vegetable species What are you working on? Do you really mean "meat", or perhaps "animal"?! ...
written 7 days ago by WouterDeCoster43k
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Answer: A: merge CNV calls from different softwares
... If your variants are in VCF format, take a look at the merge subcommand of [SURVIVOR][1] . [1]: https://github.com/fritzsedlazeck/SURVIVOR ...
written 8 days ago by WouterDeCoster43k
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Answer: A: Trimming of fasta file headers
... `cut -f1 -d' ' myfasta.fa` ...
written 9 days ago by WouterDeCoster43k
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Answer: A: How convert a fastQ file to a Sam/Bam file
... You need a reference genome against which you are going to align the reads against depending on your organism, an aligner tool that depends on your technology (like bwa mem, bowtie2). ...
written 11 days ago by WouterDeCoster43k
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Comment: C: cheap and good Hi-C protocol
... Hello Ric! We believe that this post does not fit the main topic of this site. Not bioinformatics For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with. If you disagree please tell us why in a reply below, we'll be ...
written 12 days ago by WouterDeCoster43k

Latest awards to WouterDeCoster

Scholar 6 days ago, created an answer that has been accepted. For A: hg19 exon, intron, UTR region
Good Answer 15 days ago, created an answer that was upvoted at least 5 times. For A: Merging multiple vcfs with GATK's CombineVariants
Teacher 18 days ago, created an answer with at least 3 up-votes. For A: Merging multiple vcfs with GATK's CombineVariants
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: Merging multiple vcfs with GATK's CombineVariants
Scholar 4 weeks ago, created an answer that has been accepted. For A: hg19 exon, intron, UTR region
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: Merging multiple vcfs with GATK's CombineVariants
Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Merging multiple vcfs with GATK's CombineVariants
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Merging multiple vcfs with GATK's CombineVariants
Popular Question 6 weeks ago, created a question with more than 1,000 views. For Getting edit distance from sam tags MD & NM: conceptual misunderstanding?
Appreciated 9 weeks ago, created a post with more than 5 votes. For A: Merging multiple vcfs with GATK's CombineVariants
Teacher 10 weeks ago, created an answer with at least 3 up-votes. For A: Merging multiple vcfs with GATK's CombineVariants
Scholar 11 weeks ago, created an answer that has been accepted. For A: hg19 exon, intron, UTR region
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Merging multiple vcfs with GATK's CombineVariants
Scholar 12 weeks ago, created an answer that has been accepted. For A: hg19 exon, intron, UTR region
Commentator 12 weeks ago, created a comment with at least 3 up-votes. For C: Bioinformatics freelancers needed
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Merging multiple vcfs with GATK's CombineVariants
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: Merging multiple vcfs with GATK's CombineVariants
Scholar 12 weeks ago, created an answer that has been accepted. For A: hg19 exon, intron, UTR region
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Merging multiple vcfs with GATK's CombineVariants
Scholar 3 months ago, created an answer that has been accepted. For A: hg19 exon, intron, UTR region
Appreciated 3 months ago, created a post with more than 5 votes. For A: Merging multiple vcfs with GATK's CombineVariants
Good Answer 3 months ago, created an answer that was upvoted at least 5 times. For A: Merging multiple vcfs with GATK's CombineVariants
Scholar 3 months ago, created an answer that has been accepted. For A: hg19 exon, intron, UTR region

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