User: Juke-34
Juke-34 • 1.3k
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Posts by Juke-34
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Comment:
C: maker2zff error on run
... I'm using this script fairly often and never had any issue.
Yes please provide a piece of your gff file. And check you are providing the proper file:
head -n 50 ${AUGUSTUS_GFF_ANNOTATIONS}.gff ...
written 11 days ago by
Juke-34 • 1.3k
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Comment:
C: gff3 to bed12
... Interesting,
> an attribute tag (like ID, Parent, or Name) must start with an alphabetic character.
gff3ToGenePred introduced peculiarity in the expected gff3 format that does not exist in the [official definition][1] of the format.
[1]: https://github.com/The-Sequence-Ontology/Specificat ...
written 12 days ago by
Juke-34 • 1.3k
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Comment:
C: gff3 to bed12
... So, your file looks perfectly fine. It's the most comprehensive gff3 file you can have.
Either you don't provide the proper file to your tool (check the path), or the tool expects a particular gff-like file.
Maybe the tool doesn't handle the ### and see that like an empty header? You could give a tr ...
written 13 days ago by
Juke-34 • 1.3k
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Comment:
C: gff3 to bed12
... Otherwise I have a script in perl that should do the work. It's called gff2bed.pl in the [GAAS][1] repository.
[1]: https://github.com/NBISweden/GAAS ...
written 14 days ago by
Juke-34 • 1.3k
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Comment:
C: gff3 to bed12
... Please provide us few lines of the beginning of your gff3 file. ...
written 14 days ago by
Juke-34 • 1.3k
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195
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... No they have to be on the same strand too. ...
written 16 days ago by
Juke-34 • 1.3k
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195
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... No they have to be on the same strand too. ...
written 16 days ago by
Juke-34 • 1.3k
0
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1
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195
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... Yes. before to select the longest isoform per locus, (if you have set the $overlapCheck to 1), all the features are checked for overlaps and gathered into a same locus when there is an overlap of 2 features of the same type. By the same type I mean as example an overlap between an mRNA and a tRNA wi ...
written 16 days ago by
Juke-34 • 1.3k
1
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... You need to git clone this repository: [GAAS][1]
And install the [prerequisites][2].
Then you launch the script gff3_sp_keep_longest_isoform.pl.
Actually only this script should do what you want.
--EDIT-- This will work only if you modify the line 89 of the following file: GAAS/annotation/BILS/Ha ...
written 16 days ago by
Juke-34 • 1.3k
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... I have Perl approach (two scripts to run) if you are interested in. But you need to have bioperl and few Perl modules. ...
written 16 days ago by
Juke-34 • 1.3k
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For A: Trinity strand specific: RF or FR
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For C: How to manipulate a gff or gtf file manually?
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