User: jean.elbers
jean.elbers • 740
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Posts by jean.elbers
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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.elbers • 740
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... 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.elbers • 740
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... 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.elbers • 740
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... 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.elbers • 740
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... 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.elbers • 740
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... 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.elbers • 740
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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.elbers • 740
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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.elbers • 740
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... 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.elbers • 740
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... Are you sure it is Million years ago and not Billion years ago? ...
written 8 days ago by
jean.elbers • 740
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For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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For A: What is Read Group platform??
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For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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For C: bbmap callvariants - how to add sample names, how to get 0/0 alleles back?
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