User: Juke34
Juke34 • 4.9k
- Reputation:
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- Location:
- Sweden
- Website:
- https://github.com/Juke34
- Twitter:
- @JacquesDainat
- Last seen:
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- Joined:
- 6 years, 6 months ago
- Email:
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Posts by Juke34
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... `agat_sp_filter_feature_from_kill_list.pl --gff input.gff --kill_list file.txt`
the kill list will be an ID per line ...
written 21 days ago by
Juke34 • 4.9k
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... You can use [AGAT][1]
[1]: https://github.com/NBISweden/AGAT ...
written 25 days ago by
Juke34 • 4.9k
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109
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... You can use [AGAT][1]
[1]: https://github.com/NBISweden/AGAT ...
written 25 days ago by
Juke34 • 4.9k
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... You should be able to perform this task with a tool from [AGAT][1]
[1]: https://github.com/NBISweden/AGAT ...
written 5 weeks ago by
Juke34 • 4.9k
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... Otherwise you can use agat_sp_filter_feature_by_attribute_ value.pl from [AGAT][1] for that
[1]: https://github.com/NBISweden/AGAT ...
written 9 weeks ago by
Juke34 • 4.9k
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... Maybe identical isoforms that are collapsed by IGV. Could you run your gff file through [AGAT][1] to check if there is any identical isoform?:
agat_convert_sp_gxf2gxf.pl --gff input.gff -o output.gff
[1]: https://github.com/NBISweden/AGAT ...
written 10 weeks ago by
Juke34 • 4.9k
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134
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... BWA and Bowtie2 might deal differently with IUPAC code ...
written 10 weeks ago by
Juke34 • 4.9k
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125
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Answer:
A: mitogenome annotation tool
... Maybe you will find a satisfying tool among this list: [https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/annotation_tools_mitome.md][1]
[1]: https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/annotation_tools_mitome.md ...
written 10 weeks ago by
Juke34 • 4.9k
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134
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... Is there any use of IUPAC code somewhere? Reads, assembly? ...
written 10 weeks ago by
Juke34 • 4.9k
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1
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177
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1
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... could you show few lines of the GTF file? ...
written 10 weeks ago by
Juke34 • 4.9k
Latest awards to Juke34
Appreciated
18 hours ago,
created a post with more than 5 votes.
For A: Orientation of PE reads a review of --fr --ff and --rf meanings
Popular Question
6 weeks ago,
created a question with more than 1,000 views.
For Bioinformatician in genome annotation, Uppsala, Sweden
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Bioinformatician in genome annotation, Uppsala, Sweden
Popular Question
4 months ago,
created a question with more than 1,000 views.
For Bioinformatician in genome annotation, Uppsala, Sweden
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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4 months 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
4 months ago,
created an answer that was upvoted at least 5 times.
For A: Trinity strand specific: RF or FR
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
Popular Question
5 months ago,
created a question with more than 1,000 views.
For Bioinformatician in genome annotation, Uppsala, Sweden
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Bioinformatician in genome annotation, Uppsala, Sweden
Popular Question
6 months ago,
created a question with more than 1,000 views.
For Bioinformatician in genome annotation, Uppsala, Sweden
Scholar
7 months ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
Voter
7 months ago,
voted more than 100 times.
Appreciated
7 months 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 months ago,
created an answer that was upvoted at least 5 times.
For A: Trinity strand specific: RF or FR
Popular Question
7 months ago,
created a question with more than 1,000 views.
For Bioinformatician in genome annotation, Uppsala, Sweden
Commentator
7 months ago,
created a comment with at least 3 up-votes.
For C: How to manipulate a gff or gtf file manually?
Scholar
8 months ago,
created an answer that has been accepted.
For A: How to convert exon genomic coordinates to protein coordinates
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