Moderator: WouterDeCoster

gravatar for WouterDeCoster
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Location:
Belgium
Website:
https://gigabaseorgiga...
Twitter:
wouter_decoster
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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

<prev • 7,117 results • page 2 of 712 • next >
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Comment: C: How do you find novel transcripts using GFFcompare?
... Hello chahat_u! It appears that your post has been cross-posted to another site: https://bioinformatics.stackexchange.com/questions/8992/how-to-find-novel-transcripts-using-gffcompare This is typically not recommended as it runs the risk that people in both communities spend their time helping you ...
written 3 days ago by WouterDeCoster40k
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Comment: C: Doing differential gene expression without knowing sample classes
... Either use a clustering-based approach (unbiased) to separate samples into biological groups (or into technical batch effect groups) or use some biological evidence (biased) e.g. expression of a marker gene, tumor suppressor gene,... ...
written 3 days ago by WouterDeCoster40k
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Comment: C: Pipe SamToFastq, BWA mem not working
... Could you try running the first part before the pipe and see if that works? `gatk SamToFastq -I markedadapters.bam -F /dev/stdout --CLIPPING_ATTRIBUTE XT --CLIPPING_ACTION 2 --INTERLEAVE true -NON_PF true -TMP_DIR= path/hello > mytest.fastq` If one of the steps later fails then the pipe will br ...
written 3 days ago by WouterDeCoster40k
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Comment: C: Breast oncoprotein oncogene
... If an answer was helpful you should upvote it, if the answer resolved your question you should mark it as accepted. ![Upvote|Bookmark|Accept][1] [1]: https://image.ibb.co/dfsqrx/upvote_accept_bookmark.png ...
written 3 days ago by WouterDeCoster40k
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Answer: A: A small detail when use VEP
... > the difference between hg38 and GRCh38 is only the contigs like chrx VS x, so I suppose it doesn't matter and I could choose either of the two I don't know for this tool (vcf2maf) specifically, but it definitely does matter for most tools. Always use the same reference for one project. If you ...
written 4 days ago by WouterDeCoster40k
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Comment: C: What should I use to annotate the plant genes for a VCF or a Fasta?
... No, the Manhattan plot shows the p-value per variant/position. You test each variant separately, and would also correct for multiple testing ...
written 4 days ago by WouterDeCoster40k
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Comment: C: What should I use to annotate the plant genes for a VCF or a Fasta?
... Thanks for explaining, that helps. I believe we have said this before: you cannot do a statistical test with just two samples, and therefore there is no sensible way for you to make a manhattan plot or QQ plot out of this data. Think about it: if you have 50 differences between sample A and sampl ...
written 4 days ago by WouterDeCoster40k
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Comment: C: What should I use to annotate the plant genes for a VCF or a Fasta?
... I mean this in the best way possible, but based on this question and your previous questions you have no idea what you are doing. We are happy to help with specific questions, but what you need is someone to sit next to and think about what you need to do and need to get. This question, as your prev ...
written 4 days ago by WouterDeCoster40k
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Comment: C: How to determine subtype-specific mutations?
... Sounds like a classic association study? ...
written 5 days ago by WouterDeCoster40k
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Comment: C: error while loading shared libraries: libboost_iostreams.so.1.60.0
... You could try installing boost as well with conda: https://anaconda.org/anaconda/boost ...
written 7 days ago by WouterDeCoster40k

Latest awards to WouterDeCoster

Good Answer 1 day ago, created an answer that was upvoted at least 5 times. For A: samtools sort bam file
Scholar 6 days ago, created an answer that has been accepted. For A: ChIP-Seq tag counts
Teacher 11 days ago, created an answer with at least 3 up-votes. For C: Split file not working
Teacher 14 days ago, created an answer with at least 3 up-votes. For C: Split file not working
Teacher 17 days ago, created an answer with at least 3 up-votes. For C: Split file not working
Teacher 19 days ago, created an answer with at least 3 up-votes. For C: Split file not working
Appreciated 21 days ago, created a post with more than 5 votes. For Workflow for structural variants from long read sequencing data
Teacher 22 days ago, created an answer with at least 3 up-votes. For C: Split file not working
Scholar 23 days ago, created an answer that has been accepted. For A: ChIP-Seq tag counts
Good Answer 25 days ago, created an answer that was upvoted at least 5 times. For A: splitting a SAM file
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For C: Split file not working
Scholar 4 weeks ago, created an answer that has been accepted. For A: ChIP-Seq tag counts
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Split file not working
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For C: Split file not working
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For C: Split file not working
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?
Scholar 7 weeks ago, created an answer that has been accepted. For A: ChIP-Seq tag counts
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)
Scholar 10 weeks ago, created an answer that has been accepted. For A: ChIP-Seq tag counts
Good Answer 10 weeks ago, created an answer that was upvoted at least 5 times. For A: splitting a SAM file

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