User: Juke34

gravatar for Juke34
Juke344.9k
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Sweden
Website:
https://github.com/Juke34
Twitter:
@JacquesDainat
Last seen:
an hour ago
Joined:
6 years, 6 months ago
Email:
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Posts by Juke34

<prev • 627 results • page 1 of 63 • next >
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Comment: C: How to filter a gff3 file by gene IDs
... `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 Juke344.9k
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Comment: C: How to filter a gff3 file by gene IDs
... You can use [AGAT][1] [1]: https://github.com/NBISweden/AGAT ...
written 25 days ago by Juke344.9k
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Comment: C: How to filter a gff3 file by gene IDs
... You can use [AGAT][1] [1]: https://github.com/NBISweden/AGAT ...
written 25 days ago by Juke344.9k
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Comment: C: Extract gene Name, ID, and description from gff3 file
... 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 Juke344.9k
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Comment: C: How to extract the transcripts with specific class_codes from a gtf file
... 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 Juke344.9k
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Comment: C: Difference of transcripts between my GFF file and the IGV results
... 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 Juke344.9k
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Comment: C: BWA cigar not corresponding to reality
... BWA and Bowtie2 might deal differently with IUPAC code ...
written 10 weeks ago by Juke344.9k
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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 Juke344.9k
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Comment: C: BWA cigar not corresponding to reality
... Is there any use of IUPAC code somewhere? Reads, assembly? ...
written 10 weeks ago by Juke344.9k
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Comment: C: How do I convert Hisat2 + stringtie gtf to EVM compatible gff3
... could you show few lines of the GTF file? ...
written 10 weeks ago by Juke344.9k

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
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
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
Appreciated 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
Teacher 5 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
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
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
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
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
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?
Teacher 8 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
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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