Moderator: WouterDeCoster

gravatar for WouterDeCoster
Reputation:
36,230
Status:
Trusted
Location:
Belgium
Website:
https://gigabaseorgiga...
Twitter:
wouter_decoster
Last seen:
10 hours ago
Joined:
2 years, 11 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 • 6,653 results • page 2 of 666 • next >
0
votes
3
answers
342
views
3
answers
Comment: C: why GATK makes things more complicated ?
... I just today ran GATK, which explicitly told me that a .fai file was necessary (and a couple of minutes later reminded me that a .dict file is necessary). It would be useful if it could create those by itself, indeed. ...
written 5 days ago by WouterDeCoster36k
3
votes
3
answers
342
views
3
answers
Answer: A: why GATK makes things more complicated ?
... I do not agree that it's too complicated. It's a huge ecosystem, so obviously they cannot fit everything on one manual page. They also need to support multiple versions of the tools. You cannot remove everything from GATK3.8 as soon as GATK4 is available. People rely on older versions or older setti ...
written 5 days ago by WouterDeCoster36k
0
votes
1
answer
126
views
1
answers
Comment: C: error while using edgeR( Negative counts not allowed)
... Please add a link to the dataset you are using. It may be necessary to download the reads and process those yourself. ...
written 5 days ago by WouterDeCoster36k
0
votes
1
answer
126
views
1
answers
Comment: C: error while using edgeR( Negative counts not allowed)
... From where did you get the fpkm counts...? We are bad at reading your mind so you'll have to elaborate. ...
written 5 days ago by WouterDeCoster36k
5
votes
1
answer
126
views
1
answers
Answer: A: error while using edgeR( Negative counts not allowed)
... > my data is of normalized gene expression(FPKM). You need raw counts for edgeR. Don't use any normalization. ...
written 5 days ago by WouterDeCoster36k
1
vote
0
answers
87
views
0
answers
Comment: C: Sub-sampling RNA-seq data
... I think this could be useful: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4296149/ ...
written 6 days ago by WouterDeCoster36k
0
votes
0
answers
87
views
0
answers
Comment: C: Sub-sampling RNA-seq data
... Not part of your question, but if you are interested in the expression the easiest would probably be to sample the counts file. I think all approaches are more or less the same, but you did not tell us anything about the aim of the analysis. ...
written 6 days ago by WouterDeCoster36k
0
votes
2
answers
239
views
2
answers
Comment: C: How to extract pattern matching sequences from a fasta file?
... Have you tried first to linearize your fasta file? ...
written 7 days ago by WouterDeCoster36k
0
votes
2
answers
239
views
2
answers
Comment: C: How to extract pattern matching sequences from a fasta file?
... Please add the command you used and the exact error / warning you got. ...
written 7 days ago by WouterDeCoster36k
2
votes
2
answers
239
views
2
answers
Answer: A: How to extract pattern matching sequences from a fasta file?
... Assuming you have a linear fasta file (without folded sequences on multiple lines) you can use grep with the `-A 1` option, to give you the matching line and the one after the match. Other useful options would be `-f`, `-F` and `-w`. ...
written 7 days ago by WouterDeCoster36k

Latest awards to WouterDeCoster

Teacher 2 days ago, created an answer with at least 3 up-votes. For A: mapping of rna seq read to reference seq
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: mapping of rna seq read to reference seq
Teacher 5 days ago, created an answer with at least 3 up-votes. For A: mapping of rna seq read to reference seq
Teacher 10 days ago, created an answer with at least 3 up-votes. For A: mapping of rna seq read to reference seq
Scholar 10 days ago, created an answer that has been accepted. For A: The order of part processions of RNA-Seq data
Teacher 16 days ago, created an answer with at least 3 up-votes. For A: mapping of rna seq read to reference seq
Commentator 17 days ago, created a comment with at least 3 up-votes. For C: Best RNA-Seq aligner: A comparison of mapping tools
Commentator 18 days ago, created a comment with at least 3 up-votes. For C: Best RNA-Seq aligner: A comparison of mapping tools
Commentator 24 days ago, created a comment with at least 3 up-votes. For C: GTF format that's acceptable for Tophat/Cufflinks
Commentator 24 days ago, created a comment with at least 3 up-votes. For C: Bioinformatics freelancers needed
Scholar 26 days ago, created an answer that has been accepted. For A: The order of part processions of RNA-Seq data
Appreciated 26 days ago, created a post with more than 5 votes. For Workflow for structural variants from long read sequencing data
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: mapping of rna seq read to reference seq
Teacher 26 days ago, created an answer with at least 3 up-votes. For A: mapping of rna seq read to reference seq
Commentator 26 days ago, created a comment with at least 3 up-votes. For C: Bioinformatics freelancers needed
Teacher 29 days ago, created an answer with at least 3 up-votes. For A: mapping of rna seq read to reference seq
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: mapping of rna seq read to reference seq
Teacher 4 weeks ago, created an answer with at least 3 up-votes. For A: mapping of rna seq read to reference seq
Scholar 4 weeks ago, created an answer that has been accepted. For A: The order of part processions of RNA-Seq data
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Plot number of mutations in each cancer type in VCF files?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: mapping of rna seq read to reference seq
Commentator 5 weeks ago, created a comment with at least 3 up-votes. For C: Plot number of mutations in each cancer type in VCF files?
Teacher 5 weeks ago, created an answer with at least 3 up-votes. For A: mapping of rna seq read to reference seq

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 639 users visited in the last hour