User: Juke-34

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Juke-341.3k
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Posts by Juke-34

<prev • 244 results • page 1 of 25 • next >
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Comment: C: maker2zff error on run
... I'm using this script fairly often and never had any issue. Yes please provide a piece of your gff file. And check you are providing the proper file: head -n 50 ${AUGUSTUS_GFF_ANNOTATIONS}.gff ...
written 11 days ago by Juke-341.3k
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Comment: C: gff3 to bed12
... Interesting, > an attribute tag (like ID, Parent, or Name) must start with an alphabetic character. gff3ToGenePred introduced peculiarity in the expected gff3 format that does not exist in the [official definition][1] of the format. [1]: https://github.com/The-Sequence-Ontology/Specificat ...
written 12 days ago by Juke-341.3k
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Comment: C: gff3 to bed12
... So, your file looks perfectly fine. It's the most comprehensive gff3 file you can have. Either you don't provide the proper file to your tool (check the path), or the tool expects a particular gff-like file. Maybe the tool doesn't handle the ### and see that like an empty header? You could give a tr ...
written 13 days ago by Juke-341.3k
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Comment: C: gff3 to bed12
... Otherwise I have a script in perl that should do the work. It's called gff2bed.pl in the [GAAS][1] repository. [1]: https://github.com/NBISweden/GAAS ...
written 14 days ago by Juke-341.3k
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Comment: C: gff3 to bed12
... Please provide us few lines of the beginning of your gff3 file. ...
written 14 days ago by Juke-341.3k
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Comment: C: How can I easily remove overlapping transcripts, keeping only longest transcript
... No they have to be on the same strand too. ...
written 16 days ago by Juke-341.3k
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Comment: C: How can I easily remove overlapping transcripts, keeping only longest transcript
... No they have to be on the same strand too. ...
written 16 days ago by Juke-341.3k
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Comment: C: How can I easily remove overlapping transcripts, keeping only longest transcript
... Yes. before to select the longest isoform per locus, (if you have set the $overlapCheck to 1), all the features are checked for overlaps and gathered into a same locus when there is an overlap of 2 features of the same type. By the same type I mean as example an overlap between an mRNA and a tRNA wi ...
written 16 days ago by Juke-341.3k
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Comment: C: How can I easily remove overlapping transcripts, keeping only longest transcript
... You need to git clone this repository: [GAAS][1] And install the [prerequisites][2]. Then you launch the script gff3_sp_keep_longest_isoform.pl. Actually only this script should do what you want. --EDIT-- This will work only if you modify the line 89 of the following file: GAAS/annotation/BILS/Ha ...
written 16 days ago by Juke-341.3k
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Comment: C: How can I easily remove overlapping transcripts, keeping only longest transcript
... I have Perl approach (two scripts to run) if you are interested in. But you need to have bioperl and few Perl modules. ...
written 16 days ago by Juke-341.3k

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Popular Question 29 days ago, created a question with more than 1,000 views. For Bioinformatician in genome annotation, Uppsala, Sweden
Scholar 3 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
Good Answer 7 months ago, created an answer that was upvoted at least 5 times. For A: Trinity strand specific: RF or FR
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 ?
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Scholar 11 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
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Commentator 13 months ago, created a comment with at least 3 up-votes. For C: How to manipulate a gff or gtf file manually?
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Appreciated 19 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 19 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
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Scholar 2.3 years ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
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