User: Juke-34

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Juke-341.1k
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Posts by Juke-34

<prev • 196 results • page 1 of 20 • next >
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Comment: C: Maker failure on almost all contig
... BTW be careful using stringtie gff3 output, maker doesn't complain but it is not use if it is given as an gff alignment (est_gff or altest_gff). ...
written 14 days ago by Juke-341.1k
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Comment: C: Maker failure on almost all contig
... Remove all the gff3 and add them one by one, doing a run each time (just the time for the tool to parse the gff3 input) to see which one raise the error. Then show us some lines of this file. ...
written 14 days ago by Juke-341.1k
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Comment: C: Maker failure on almost all contig
... If you deactivate/remove it, does it work again properly ? ...
written 15 days ago by Juke-341.1k
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Comment: C: Maker failure on almost all contig
... Ok, so how did you input the augustus data ? ...
written 15 days ago by Juke-341.1k
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Comment: C: Maker failure on almost all contig
... Are you sure these contig names are unique within the fasta file ? ...
written 15 days ago by Juke-341.1k
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Comment: C: Maker failure on almost all contig
... Can you show us a contig name of one that failed ? Then, could you provide as well a piece of the gff3 you use ? ...
written 15 days ago by Juke-341.1k
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Answer: A: Best method to submit an annotated prokaryotic genome in NCBI
... You could use the beta version of the NCBI gff submission (it looks a bit painful). Or convert your data into EMBL and submit to the european nucleotide archive (ENA) using [EMBLmyGFF3][1] Or convert your data into EMBL and then convert to genebank and then submit to NCBI. [1]: https://github.com ...
written 16 days ago by Juke-341.1k
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Comment: C: How to generate corresponding embl file with gff and fasta file of each scaffold
... Thank you very much for your feedback. I will try to improve the help. Actually I mixed up the different terms. When you said "ID" I thought "locus_tag". I just realised you were talking about the ID line... My fault. So, yes there is no way to have the contig name into the ID line otherwise it will ...
written 21 days ago by Juke-341.1k
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Comment: C: phytozome gtf file
... You can download it and share it by dropbox ...
written 21 days ago by Juke-341.1k
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Comment: C: How to generate corresponding embl file with gff and fasta file of each scaffold
... Excellent, could you share your trick ? ...
written 21 days ago by Juke-341.1k

Latest awards to Juke-34

Scholar 21 days ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Teacher 21 days ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Teacher 24 days ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Commentator 8 weeks ago, created a comment with at least 3 up-votes. For C: How to manipulate a gff or gtf file manually?
Guru 8 weeks ago, received more than 100 upvotes.
Appreciated 8 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 8 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Popular Question 8 months ago, created a question with more than 1,000 views. For Emboss seqret - problem conversion gff+fasta to EMBL
Teacher 12 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Centurion 16 months ago, created 100 posts.
Scholar 17 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Scholar 23 months ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names
Teacher 23 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Scholar 2.2 years ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names
Teacher 2.2 years ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Scholar 2.5 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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