User: Juke-34
Juke-34 • 3.7k
- Reputation:
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Posts by Juke-34
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... 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-34 • 3.7k
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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-34 • 3.7k
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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-34 • 3.7k
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... From Hisat bam file you can run bam2hints ...
written 2 days ago by
Juke-34 • 3.7k
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... 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-34 • 3.7k
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... 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-34 • 3.7k
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... 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-34 • 3.7k
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... Yes you're right, thank you for pointing it. ...
written 8 days ago by
Juke-34 • 3.7k
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509
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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-34 • 3.7k
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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-34 • 3.7k
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For A: How to convert exon genomic coordinates to protein coordinates
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For A: Trinity strand specific: RF or FR
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For A: How to convert exon genomic coordinates to protein coordinates
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For A: How to convert exon genomic coordinates to protein coordinates
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For A: Orientation of PE reads a review of --fr --ff and --rf meanings
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For A: Trinity strand specific: RF or FR
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For A: How to convert exon genomic coordinates to protein coordinates
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For A: How to convert exon genomic coordinates to protein coordinates
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