User: Juke34

gravatar for Juke34
Juke344.8k
Reputation:
4,820
Status:
Trusted
Location:
Sweden
Website:
https://github.com/Juke34
Twitter:
@JacquesDainat
Last seen:
an hour ago
Joined:
6 years, 3 months ago
Email:
j*************@gmail.com

Posts by Juke34

<prev • 603 results • page 1 of 61 • next >
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Comment: C: Strandness setting for HISAT2 : BGI sequencing platform
... Run [GUESSmyLT][1] and you should have your answer. [1]: https://github.com/NBISweden/GUESSmyLT ...
written 2 days ago by Juke344.8k
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Answer: A: [Prokaryote] How to go from reads to counts given that there is no exon column i
... You can use agat_convert_sp_gxf2gxf.pl from [AGAT][1] , it will re-create the exon features [1]: https://github.com/NBISweden/AGAT ...
written 9 days ago by Juke344.8k
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Comment: C: Converting GFF to GTF
... If it is not the term expected by the GTF format, AGAT should automatically convert them to the proper one. ...
written 10 days ago by Juke344.8k
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Answer: A: Count number of Genes in GFF3 file (Prokka output)
... You can use `agat_sp_statistics.pl ` from [AGAT][1] [1]: https://github.com/NBISweden/AGAT ...
written 10 days ago by Juke344.8k
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Answer: A: Cutting fasta file into chunks?
... Plenty of solution described here : [Tutorial: FASTA file split][1] [1]: https://www.biostars.org/p/443190/#443245 ...
written 12 days ago by Juke344.8k
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Comment: C: AGAT - Another Gff Analysis Toolkit
... If they are identical in all points another isoform I don't see the reason to keep it. It is most likely an error while creating the file/annotation. It should not make any difference for genes quantification. For transcripts well the isoforms removed will not have any counts because they will be ab ...
written 15 days ago by Juke344.8k
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Comment: C: SamReadViewer - A small utility to visualise read alignment directly from sam fo
... The code itself to build the ref from CIGAR+MD is from minimap2. So all the credits should go to the minimap2 developers ^^. ...
written 19 days ago by Juke344.8k
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Comment: C: SamReadViewer - A small utility to visualise read alignment directly from sam fo
... Thx, I was hoping so but I start to doubt according to the really few feedback I got (from twitter and here) ...
written 19 days ago by Juke344.8k
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Comment: C: SamReadViewer - A small utility to visualise read alignment directly from sam fo
... Thx, I was hoping so but I start to doubt according to the really few feedback I got (from twitter and here) ...
written 19 days ago by Juke344.8k
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Comment: C: SamReadViewer - A small utility to visualise read alignment directly from sam fo
... Yes it mentioned on the tool page. ```This utility makes it easy to visualise a read alignment against its reference without the reference. Indeed the reference is re-created based on the CIGAR string + the MD tag.``` But maybe it is not clear enough. The tool give also a warning if the MD ta ...
written 22 days ago by Juke344.8k

Latest awards to Juke34

Teacher 16 days ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Bioinformatician in genome annotation, Uppsala, Sweden
Popular Question 7 weeks ago, created a question with more than 1,000 views. For Bioinformatician in genome annotation, Uppsala, Sweden
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Appreciated 8 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 8 weeks ago, created an answer that was upvoted at least 5 times. For A: Trinity strand specific: RF or FR
Scholar 9 weeks ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Teacher 9 weeks ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Scholar 10 weeks ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Bioinformatician in genome annotation, Uppsala, Sweden
Popular Question 3 months 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
Teacher 3 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Popular Question 3 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
Voter 4 months ago, voted more than 100 times.
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 4 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
Commentator 4 months ago, created a comment with at least 3 up-votes. For C: How to manipulate a gff or gtf file manually?
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
Scholar 5 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates

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