User: jean.elbers

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jean.elbers1.5k
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Posts by jean.elbers

<prev • 208 results • page 1 of 21 • next >
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Comment: C: Problem with genome assembly de novo on STACKS
... Please provide more information. From the description it sounds like you are doing de novo genome assembly, but I can only assume you mean you are de novo assembling your RAD-Seq type reads with the de novo pipeline in STACKS (also not sure of the version of STACKS you are using or what commands you ...
written 22 days ago by jean.elbers1.5k
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Comment: C: Imputation on low coverage samples
... Are these human samples? If not do you have a custom reference panel for your organism? ...
written 22 days ago by jean.elbers1.5k
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Comment: C: Create Chain File for Converting Genome Coordinates
... `bcftools consensus` has a `--chain` option. (at least for version 1.10.2) -c, --chain write a chain file for liftover Have no idea regarding how well it would work for your purposes. ...
written 6 weeks ago by jean.elbers1.5k
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Comment: C: Create Chain File for Converting Genome Coordinates
... While `Liftoff` (https://github.com/agshumate/Liftoff) doesn't make a chain file, it is another program for lifting over annotations that is under GPL-3.0 license. Please contact your legal department to verify if you could use that and its dependencies. ...
written 8 weeks ago by jean.elbers1.5k
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Comment: C: Using HiCanu assembler on PacBio Hifi reads
... HiCanu is certainly customizable for assemblies- I didn't get good results with the default settings when I tried it several months ago on a development branch, but it can generate amazing assemblies by tweaking the settings. The same goes for "normalCanu". ...
written 11 weeks ago by jean.elbers1.5k
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Comment: C: Using HiCanu assembler on PacBio Hifi reads
... I haven't tried HiCanu in several months, so not sure if settings have changed to advise you (it was a development branch I was using at the time). You can also try hifiasm (https://github.com/chhylp123/hifiasm) first to get an idea of what HiCanu might give you before you optimize the settings for ...
written 3 months ago by jean.elbers1.5k
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Answer: C: BBMap Clumpify error
... Can you try ~/bbmap/clumpify.sh in1=xx.r_1.fq.gz in2=xx.r_2.fq.gz out1=xx.clumped1.fq.gz out2=xx.clumped2.fq.gz reorder=f I am pretty sure the BBMap scripts don't like spaces next to the arguments. Update @Genomax beat me to it. ...
written 5 months ago by jean.elbers1.5k
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Comment: C: Demultiplexing Issue on Lexogen's QuantSeq 3' mRNASeq ran in NextSeq550
... Not an answer to your question, but It seems like you should contact Lexogen technical support as well. ...
written 6 months ago by jean.elbers1.5k
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Comment: C: Mapping (minimap2) nanopore reads to parent species to confirm hybridization
... How "related" are the two parent species? Do you expect to have F1 hybrid progeny (~50% parent1: ~50% parent2) or backcrosses? I would recommend simultaneous "mapping" (although the tool I suggest using, `seal.sh` from `BBTools/BBMap`, is really not aligning - rather classifying by k-mers). Because ...
written 7 months ago by jean.elbers1.5k
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Comment: C: Where to upload protein coding gene annotation ?
... I wouldn't say I work a lot with annotation- I merely have some experience. I have never used ENA, but I must say that fulfilling annotation requirements set by NCBI may require a few messages back and forth with the curators. As far as I can tell, most people don't submit structural or functional a ...
written 8 months ago by jean.elbers1.5k

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