User: Juke-34
Juke-34 • 1.0k
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- 3 years, 2 months ago
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Posts by Juke-34
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... It would be probably easier in that case to convert the gff output file into EMBL flat file with [gff3toembl][1] or [EMBLmyGFF3][2] and submit it to the european database [ENA][3], which is part to the INSDC.
[1]: https://github.com/sanger-pathogens/gff3toembl
[2]: https://github.com/NBISweden ...
written 10 hours ago by
Juke-34 • 1.0k
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... That seems to be correct. If you haven't seen any error message, it means that your proteins are not related to any pathway signature. ...
written 4 days ago by
Juke-34 • 1.0k
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... It looks like the issue is due to an unprintable character. Have you manipulated the file with Windows at some point ? ...
written 6 days ago by
Juke-34 • 1.0k
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... Did you try the -fix_nucleotides parameter while running Maker ? ...
written 6 days ago by
Juke-34 • 1.0k
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... Probably because there is no gene feature. I guess the converters expect those features.
I had so many issues during the past years with the different gff3 files you can find everywhere. There is often something missing for the tools that use gff3 as input. So, I decided to write a parser that work ...
written 6 days ago by
Juke-34 • 1.0k
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... What kind of manual manipulation are you doing ? It is not really the kind of file that we like to modify manually...
I load huge genome into text editor without any problem using "sublime". I guess using "atom" it will work well too. ...
written 7 days ago by
Juke-34 • 1.0k
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Comment:
C: GFF3 to EMBL
... Ok it ended we change the name into EMBLmyGFF3.
...
written 18 days ago by
Juke-34 • 1.0k
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Comment:
C: GFF3 to EMBL
... Yes you're right but I didn't find any name satisfactory, so I decided to keep this name even if it is ambiguous with the other tool. I hope it will be findable among the vast internet world thanks to the key words. ...
written 26 days ago by
Juke-34 • 1.0k
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Comment:
C: GFF3 to EMBL
... Yes we know, it's because it is supposed to perform the same work except that the tool you cite handles only the gff3 flavor of the Prokka tool, and ours can be tuned to handle any kind of gff3 annotation file.
Here is the reason why we developed our tool. ...
written 27 days ago by
Juke-34 • 1.0k
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Tool:
GFF3 to EMBL converter
... We developed a universal GFF3 to EMBL format convertor called EMBLmyGFF3.
This software allows to convert GFF3 and FASTA to legal EMBL format suitable for ENA submission.
Here the address of the repository: http://github.com/NBISweden/EMBLmyGFF3 ...
written 28 days ago by
Juke-34 • 1.0k
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7 days ago,
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For C: How to manipulate a gff or gtf file manually?
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6 months ago,
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For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
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For A: Where is it possible to submit annotated eukaryote genomes?
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For Emboss seqret - problem conversion gff+fasta to EMBL
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For A: Where is it possible to submit annotated eukaryote genomes?
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For A: How to convert exon genomic coordinates to protein coordinates
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For A: Extract fasta sequences from a large file using a list of names
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