User: jean.elbers
jean.elbers • 1.3k
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Posts by jean.elbers
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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 8 days ago by
jean.elbers • 1.3k
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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 8 days ago by
jean.elbers • 1.3k
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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 8 days ago by
jean.elbers • 1.3k
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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 8 days ago by
jean.elbers • 1.3k
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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 9 days ago by
jean.elbers • 1.3k
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... 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 9 days ago by
jean.elbers • 1.3k
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... You are welcome! Glad to help! ...
written 10 days ago by
jean.elbers • 1.3k
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... Try it one more time. I forgot to change the `bedtools getfasta` command to force strandness with the `-s` option. ...
written 10 days ago by
jean.elbers • 1.3k
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... Try the following updated code:
makeblastdb -in reference.fa -dbtype nucl
samtools faidx reference.fa
cut -f 1,2 reference.fa.fai > chrom.sizes
blastn -db reference -query query.fasta -outfmt 6 -out query.fasta-against-reference.blast
cut -f 2,9,10 query.fasta-against-refere ...
written 11 days ago by
jean.elbers • 1.3k
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... This is very strange indeed. I am wondering if it has something to do with a bug in Bedtools (by the way, what version of bedtools are you using?)
Just for kicks, can you check the following:
samtools faidx reference.fa Sequence1:484754-484980
It should produce
>Sequence1:484754-4849 ...
written 11 days ago by
jean.elbers • 1.3k
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