User: Juke-34

gravatar for Juke-34
Juke-341.0k
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Sweden
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6 hours ago
Joined:
3 years, 2 months ago
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j*************@gmail.com

Posts by Juke-34

<prev • 179 results • page 1 of 18 • next >
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Comment: C: Error duirng the creation of .sqn file for the submission to NCBI
... It would be probably easier in that case to convert the gff output file into EMBL flat file with [gff3toembl][1] or [EMBLmyGFF3][2] and submit it to the european database [ENA][3], which is part to the INSDC. [1]: https://github.com/sanger-pathogens/gff3toembl [2]: https://github.com/NBISweden ...
written 10 hours ago by Juke-341.0k
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Answer: A: InterProScan (v5) to get pathway annotation
... That seems to be correct. If you haven't seen any error message, it means that your proteins are not related to any pathway signature. ...
written 4 days ago by Juke-341.0k
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Comment: C: Augustus/Maker2 failing due to invalid nucleotides in sequence
... It looks like the issue is due to an unprintable character. Have you manipulated the file with Windows at some point ? ...
written 6 days ago by Juke-341.0k
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Comment: C: Augustus/Maker2 failing due to invalid nucleotides in sequence
... Did you try the -fix_nucleotides parameter while running Maker ? ...
written 6 days ago by Juke-341.0k
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Comment: C: GFF3 file incompatibilities (source: BRAD)
... Probably because there is no gene feature. I guess the converters expect those features. I had so many issues during the past years with the different gff3 files you can find everywhere. There is often something missing for the tools that use gff3 as input. So, I decided to write a parser that work ...
written 6 days ago by Juke-341.0k
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Comment: C: How to manipulate a gff or gtf file manually?
... What kind of manual manipulation are you doing ? It is not really the kind of file that we like to modify manually... I load huge genome into text editor without any problem using "sublime". I guess using "atom" it will work well too. ...
written 7 days ago by Juke-341.0k
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Comment: C: GFF3 to EMBL
... Ok it ended we change the name into EMBLmyGFF3. ...
written 18 days ago by Juke-341.0k
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Comment: C: GFF3 to EMBL
... Yes you're right but I didn't find any name satisfactory, so I decided to keep this name even if it is ambiguous with the other tool. I hope it will be findable among the vast internet world thanks to the key words. ...
written 26 days ago by Juke-341.0k
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Comment: C: GFF3 to EMBL
... Yes we know, it's because it is supposed to perform the same work except that the tool you cite handles only the gff3 flavor of the Prokka tool, and ours can be tuned to handle any kind of gff3 annotation file. Here is the reason why we developed our tool. ...
written 27 days ago by Juke-341.0k
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Tool: GFF3 to EMBL converter
... We developed a universal GFF3 to EMBL format convertor called EMBLmyGFF3. This software allows to convert GFF3 and FASTA to legal EMBL format suitable for ENA submission. Here the address of the repository: http://github.com/NBISweden/EMBLmyGFF3 ...
tool gff3 annotation embl conversion submission written 28 days ago by Juke-341.0k

Latest awards to Juke-34

Commentator 7 days ago, created a comment with at least 3 up-votes. For C: How to manipulate a gff or gtf file manually?
Guru 7 days ago, received more than 100 upvotes.
Appreciated 6 months ago, created a post with more than 5 votes. For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Popular Question 7 months ago, created a question with more than 1,000 views. For Emboss seqret - problem conversion gff+fasta to EMBL
Teacher 10 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Centurion 15 months ago, created 100 posts.
Scholar 15 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Scholar 21 months ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names
Teacher 22 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Scholar 2.1 years ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names
Teacher 2.1 years ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Scholar 2.4 years ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names

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