User: jean.elbers

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Posts by jean.elbers

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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 9 days ago by jean.elbers1.4k
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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 23 days ago by jean.elbers1.4k
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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.elbers1.4k
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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 4 months ago by jean.elbers1.4k
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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 4 months ago by jean.elbers1.4k
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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 5 months ago by jean.elbers1.4k
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Comment: C: Where to upload protein coding gene annotation ?
... 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.elbers1.4k
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Comment: C: Less and less genes predicted with each iteration of SNAP/MAKER
... 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.elbers1.4k
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Comment: C: Less and less genes predicted with each iteration of SNAP/MAKER
... 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.elbers1.4k
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Comment: C: Less and less genes predicted with each iteration of SNAP/MAKER
... @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.elbers1.4k

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