User: Juke34
Juke34 • 4.5k
- Reputation:
- 4,450
- Status:
- Trusted
- Location:
- Sweden
- Website:
- https://github.com/Juke34
- Twitter:
- @JacquesDainat
- Last seen:
- an hour ago
- Joined:
- 6 years, 1 month ago
- Email:
- j*************@gmail.com
Posts by Juke34
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answer
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Comment:
C: Maker Annotation Error
... Use a `sed` command in a terminal ...
written 13 days ago by
Juke34 • 4.5k
0
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1
answer
86
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1
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Comment:
C: Maker Annotation Error
... Look at your sequence to see why you have the letter O. If it looks ok (actually part of the sequence) then replace it by N. ...
written 14 days ago by
Juke34 • 4.5k
1
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94
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answers
... You can also try other solutions to perform your conversion. See a mini-review [here][1].
To be sure that the `exon feature found before transcript ID` is not lost you can check with an `awk` command or with `agat_sq_stat_basic.pl` from [AGAT][2] if all the exons from the GFF file are still present ...
written 20 days ago by
Juke34 • 4.5k
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84
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Tutorial:
Sorting GFF/GTF files
... How to sort a GFF/GTF file?
I saw this question many times and the answer is not simple because those formats can be sorted in different ways.
I made a mini-review of common tools manipulating GFF/GTF to see how they sort the files:
https://github.com/NBISweden/AGAT/wiki/Topological-sorting-of-gf ...
written 20 days ago by
Juke34 • 4.5k
1
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5
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5
answers
... When asking GTF format from `agat_convert_sp_gxf2gxf.pl`, it is the Bioperl converter that is used. Currently this converter is not perfect. I plan to fix the problem in Bioperl one day.
The best is to use `agat_convert_sp_gff2gtf.pl`. You can find a comparison to other tools [here][1]
I suggest y ...
0
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Comment:
C: Standardizing 3rd party GFF3 file
... Which AGAT version do you use? I would suggest to install the most up-to-date in the master branch.
Your file sounds quite complex. You should run `agat_convert_sp_gxf2gxf.pl` first to point the potential problem. I think you will have to "drive" AGAT to behave properly.
I would probably split you ...
written 25 days ago by
Juke34 • 4.5k
0
votes
1
answer
174
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... Hi,
I'm the AGAT's developer. I'm wondering if there is anything I could improve (except installation). I don't really get what was the specific format/attribute expected by featurecount that was missing. Could you show a record (all features linked to each other by some relationship, e.g gene/trans ...
written 4 weeks ago by
Juke34 • 4.5k
1
vote
2
answers
105
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2
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... You can find a comprehensive list of annotation tools here: [https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/annotation_tools.md][1].
Very few tools give confidence score to the predictions, MAKER is one the rare one. Otherwise you can use MAKER to add the confidence score over ...
written 4 weeks ago by
Juke34 • 4.5k
0
votes
3
answers
321
views
3
answers
... You can try [AGAT][1] it might fix your problem
[1]: https://github.com/NBISweden/AGAT ...
written 5 weeks ago by
Juke34 • 4.5k
0
votes
3
answers
144
views
3
answers
... Several solutions (None in R) documented in this [mini-review][1]
[1]: https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/split_fasta.md ...
written 5 weeks ago by
Juke34 • 4.5k
Latest awards to Juke34
Popular Question
16 days ago,
created a question with more than 1,000 views.
For Bioinformatician in genome annotation, Uppsala, Sweden
Popular Question
28 days ago,
created a question with more than 1,000 views.
For Bioinformatician in genome annotation, Uppsala, Sweden
Scholar
7 weeks ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Voter
7 weeks ago,
voted more than 100 times.
Appreciated
7 weeks ago,
created a post with more than 5 votes.
For A: Orientation of PE reads a review of --fr --ff and --rf meanings
Good Answer
7 weeks ago,
created an answer that was upvoted at least 5 times.
For A: Trinity strand specific: RF or FR
Popular Question
8 weeks ago,
created a question with more than 1,000 views.
For Bioinformatician in genome annotation, Uppsala, Sweden
Commentator
8 weeks ago,
created a comment with at least 3 up-votes.
For C: How to manipulate a gff or gtf file manually?
Scholar
12 weeks ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Scholar
3 months ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Scholar
3 months ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Appreciated
3 months ago,
created a post with more than 5 votes.
For A: Orientation of PE reads a review of --fr --ff and --rf meanings
Appreciated
3 months ago,
created a post with more than 5 votes.
For A: Orientation of PE reads a review of --fr --ff and --rf meanings
Scholar
3 months ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Scholar
3 months ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Good Answer
4 months ago,
created an answer that was upvoted at least 5 times.
For A: Trinity strand specific: RF or FR
Scholar
4 months ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Scholar
4 months ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
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