User: jean.elbers
jean.elbers • 1.4k
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Posts by jean.elbers
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... 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 9 days ago by
jean.elbers • 1.4k
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... 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 23 days ago by
jean.elbers • 1.4k
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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 3 months ago by
jean.elbers • 1.4k
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... Not an answer to your question, but It seems like you should contact Lexogen technical support as well. ...
written 4 months ago by
jean.elbers • 1.4k
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... 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 4 months ago by
jean.elbers • 1.4k
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... 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 5 months ago by
jean.elbers • 1.4k
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... Submitting structural annotations to NCBI is okay, but submitting functional annotations is quite another thing. There is a tool https://genomeannotation.github.io/GAG/ that will help with both, but the functional annotation part is very difficult to go from MAKER annotations to those accepted by NC ...
written 5 months ago by
jean.elbers • 1.4k
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... No, you were correct that I only showed AED-only filtering steps in the analysis steps, but there were some attempts at combining AED filtering, redundancy removal, and randomization as well that I didn't document but tried. ...
written 5 months ago by
jean.elbers • 1.4k
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... Well, I had also tried many different things- some similar steps to your pipeline (ex: redundancy removal) and other things (ex:AED filtering, redundancy removal, and randomization), etc. Still to no avail. ...
written 5 months ago by
jean.elbers • 1.4k
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... @Juke-34 Thank you for the links. You are probably doing a much better job than I have done with training Augustus with MAKER predictions. I have always found the opposite between BUSCO and MAKER training Augustus, but that is at least for mammals and one turtle (Kemp's Ridley sea turtle, marsh rice ...
written 5 months ago by
jean.elbers • 1.4k
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