User: Juke-34

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Juke-343.7k
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Posts by Juke-34

<prev • 501 results • page 1 of 51 • next >
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Comment: C: Ensembl and Gene Prediction Tools output CDS' not divisible by 3
... I agree but I would say this is quite unlikely. As I show [here][1] 1-based system is one of the rare thing that was well defined since the beginning of the format in 1997 i.e `Integers. must be less than or equal to . Sequence numbering starts at 1, so these numbers should be between 1 and the len ...
written 1 day ago by Juke-343.7k
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Comment: C: EBI submission and AGP ?
... I guess the difference will be when applying filters to request assemblies. There is probably a way to download contig either scaffold. When asking for contigs in your case it will not be contigs in reality... The best would be to contact their Helpdesk and describe your case, they will tell you ho ...
written 1 day ago by Juke-343.7k
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Comment: C: EBI submission and AGP ?
... Using fasta2agp.pl will make a fake agp file describing the current state of the assembly (no change between contig and scaffold). This is cheating but it should be accepted by ENA. There is no other solution except re-doing everything from scratch. If you choose to do this 'fake' agp, think to add ...
written 2 days ago by Juke-343.7k
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Comment: C: StringTie output to train Augustus
... From Hisat bam file you can run bam2hints ...
written 2 days ago by Juke-343.7k
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Answer: A: Ensembl and Gene Prediction Tools output CDS' not divisible by 3
... GFF is one-based coordinate. See here [https://www.biostars.org/p/84686/][1]. So it is 1828 - 686 +1 = 1143 1143 / 3 = 381 [1]: https://www.biostars.org/p/84686/ ...
written 2 days ago by Juke-343.7k
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Comment: C: StringTie output to train Augustus
... have a look here https://github.com/ikmb-denbi/genome-annotation they produce a lot of different evidence to feed Augustus. They have a lot of utilities to produce hints from gtf/gff ...
written 3 days ago by Juke-343.7k
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Answer: A: gene set filter/selection for training ab initio annotation tools
... For whom interested we also have a nextflow pipeline for it that goes even beyond ( does the training too ). You can find it here: [https://github.com/NBISweden/pipelines-nextflow/tree/master/AbinitioTraining][1] [1]: https://github.com/NBISweden/pipelines-nextflow/tree/master/AbinitioTraining ...
written 8 days ago by Juke-343.7k
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Comment: C: gene set filter/selection for training ab initio annotation tools
... Yes you're right, thank you for pointing it. ...
written 8 days ago by Juke-343.7k
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Comment: C: Create de novo repeat library
... actually Dfam.hmm is needed only if you use nhmmer in repeatmasker as search engine. Otherwise it will be the Dfam.embl file to use. Then you need buildRMLibFromEMBL.pl to create the Fasta file from it and then you run `makeblastdb -dbtyp nucl ...` ...
written 11 days ago by Juke-343.7k
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Comment: C: Repeatmodeler keeps dying
... everything is fine in this log, what is your problem? ...
written 11 days ago by Juke-343.7k

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Scholar 1 day ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
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Scholar 12 days ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
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Scholar 5 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Scholar 5 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
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Prophet 8 months ago, created a post with more than 20 followers. For Orientation of PE reads a review of --fr --ff and --rf meanings
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Scholar 11 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Scholar 12 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates

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