User: jean.elbers

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jean.elbers740
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Posts by jean.elbers

<prev • 100 results • page 1 of 10 • next >
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Comment: C: Error while running SNPEff
... Maybe try increasing the stack size (see https://examples.javacodegeeks.com/java-basics/exceptions/java-lang-stackoverflowerror-how-to-solve-stackoverflowerror/) java -Xss1M -jar snpEff.jar build -gtf22 -v PBW Or increase `-Xss` to something larger if `-Xss1M` doesn't work. ...
written 19 hours ago by jean.elbers740
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Comment: C: Your favourite workflow for Hi-C data analysis (Plant Genome)
... I am not sure about plant genomes, but here is a guide for `3d-dna` and related tools integrating Hi-C reads into *de novo* assembly (http://aidenlab.org/assembly/manual_180322.pdf) ...
written 2 days ago by jean.elbers740
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Comment: C: views on vgteam codebase on gituhb?
... are you talking about `https://github.com/vgteam/vg`? Not sure someone give you a "quick" rundown of the src code. There are several publications associated with `vg` that might help. ...
written 2 days ago by jean.elbers740
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Comment: C: How to make interval list for GBS sequencing?
... I don't think it would be inappropriate for variant-calling per se, but I wonder about the down-stream analysis leading up to GATK variant calling. Others with more knowledge could pipe in if you make a separate thread or quickly Google pros and cons of reduced-representation analysis pipelines vers ...
written 2 days ago by jean.elbers740
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Comment: C: How to make interval list for GBS sequencing?
... If I understand you correctly, you are analyzing your Genotyping-by-sequencing data with GATK? I think it might be prudent to use a reduced-representation analysis method such as `STACKS` (http://catchenlab.life.illinois.edu/stacks/) or `ipyrad`(https://ipyrad.readthedocs.io/) for this purpose. ...
written 2 days ago by jean.elbers740
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Comment: C: Quality control after genotype imputation
... So, someone else chimed in on `BEAGLE` post imputation quality control, see https://www.biostars.org/p/148675/#369605 ...
written 7 days ago by jean.elbers740
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Comment: C: All SNPs excluded with LD pruning
... Hmmm, you have `ld.threshold=0.2`, whilst in text you reference they say `LD pruned (LD threshold: 1.0)`. Also, I wonder if there should be some sort of correction for multiple tests (i.e., using a false discovery rate to lower the LD threshold)? ...
written 7 days ago by jean.elbers740
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Comment: C: RadSeq and short read
... What is the objective of the RADseq project you are working on? Might I suggest `STACKS` (http://catchenlab.life.illinois.edu/stacks/) or `ipyrad` (https://ipyrad.readthedocs.io/) or `dDocent` (http://www.ddocent.com/) for the analysis? ...
written 7 days ago by jean.elbers740
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Comment: C: Program for Amplicon (MHC) Analysis?
... Interesting. Are those data (your SOSP MHC) published? It might make for an interesting comparison when we eventually try to publish ours. ...
written 8 days ago by jean.elbers740
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Comment: C: Calibration of Ultramatric species phylogeny tree?
... Are you sure it is Million years ago and not Billion years ago? ...
written 8 days ago by jean.elbers740

Latest awards to jean.elbers

Scholar 13 days ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Appreciated 23 days ago, created a post with more than 5 votes. For C: Racon-Illumina or Pilon?
Scholar 4 weeks ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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Scholar 5 weeks ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Scholar 4 months ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Scholar 5 months ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
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Scholar 11 months ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: What is Read Group platform??
Scholar 12 months ago, created an answer that has been accepted. For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?

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