User: jean.elbers

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Posts by jean.elbers

<prev • 211 results • page 2 of 22 • next >
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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 8 months ago by jean.elbers1.5k
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Answer: 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 8 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 10 months ago by jean.elbers1.5k
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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 10 months ago by jean.elbers1.5k
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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 10 months ago by jean.elbers1.5k
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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 10 months ago by jean.elbers1.5k
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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 10 months ago by jean.elbers1.5k
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Comment: C: Less and less genes predicted with each iteration of SNAP/MAKER
... Unfortunately, sometimes you can "overtrain" your ab initio gene predictors. More information can be found through searches through the MAKER Developer Google group https://groups.google.com/forum/#!forum/maker-devel. I really don't have much experience with SNAP, rather Augustus. Training Augustus ...
written 10 months ago by jean.elbers1.5k
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Comment: C: Extract flanking region of -500 nt upstream and downstream of BLAST result on ge
... You are welcome! Glad to help! ...
written 10 months ago by jean.elbers1.5k
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Comment: C: Extract flanking region of -500 nt upstream and downstream of BLAST result on ge
... Try it one more time. I forgot to change the `bedtools getfasta` command to force strandness with the `-s` option. ...
written 10 months ago by jean.elbers1.5k

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