User: Juke-34

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Juke-343.2k
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Posts by Juke-34

<prev • 421 results • page 1 of 43 • next >
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Answer: A: Alternatives to RepeatModeler / nseg install fail
... I have added `nseg` in bioconda, you can install it using bioconda now. ...
written 3 days ago by Juke-343.2k
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Comment: C: replace gene names in gff file
... Ya I implemented like that to follow what does Ensembl. What you could do now that your file is standardized by AGAT, is to use agat_sq_manage_ID.pl (Do not use this script with your original file because it expects a properly formatted gff3. All script with sq prefix need a proper gff3 file ) ...
written 4 days ago by Juke-343.2k
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Answer: A: replace gene names in gff file
... I would suggest to use `agat_sp_manage_IDs.pl` from [AGAT][1]. In same time it will standardize your output file which is not correct (9th column should contain ’tag value’ attribute and it is not the case for gene and transcript) [1]: https://github.com/NBISweden/AGAT ...
written 5 days ago by Juke-343.2k
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Tutorial: Create de novo repeat library
... **Tutorial for de-novo repeat library construction** The RepeatMasker software includes a lot repeat library. You can query them using: queryTaxonomyDatabase.pl -h queryRepeatDatabase.pl -h If there is no repeat library available for your species, you may want to create your own. * ...
de-novo annotation repeat tutorial written 7 days ago by Juke-343.2k
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Answer: A: Alternatives to RepeatModeler / nseg install fail
... To install nseg (Wooton and Federhen, 1993; see ftp://ftp.ncbi.nih.gov/pub/seg/nseg. I'm currently trying to fix the bioconda recipe... ...
written 8 days ago by Juke-343.2k
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Answer: C: changing ID in an existing GFF3 file
... You can try with `agat_sp_manage_IDs.pl` from [AGAT][1] [1]: https://github.com/NBISweden/AGAT ...
written 8 days ago by Juke-343.2k
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Answer: A: GTF to GFF conversion
... You can try [AGAT][1] with `agat_sp_gxf_to_gff3.pl` [1]: https://github.com/NBISweden/AGAT ...
written 10 days ago by Juke-343.2k
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Answer: A: de novo transcriptome annotation steps
... In my sense the hard part is the assembly not the annotation. As it is supposed to be mature RNA it is just matter to find the correct orf. I would go for [transdecoder][1], and interproscan on the proteome you will get. [1]: https://github.com/TransDecoder/TransDecoder/wiki ...
written 13 days ago by Juke-343.2k
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Comment: C: Duplicated CDS start/stop entries in GFF-file
... it is available as conda package so you don't care it is in perl ;) ...
written 13 days ago by Juke-343.2k
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Answer: A: Duplicated CDS start/stop entries in GFF-file
... It is not duplicate entries they are just isoforms... You can use `agat_sp_keep_longest_isoform.pl` from [AGAT](https://github.com/NBISweden/AGAT) if you wish to filter the annotation and keep only le longest isoform per locus. Then you can extract the start codons: `agat_sp_extract_sequences ...
written 13 days ago by Juke-343.2k

Latest awards to Juke-34

Appreciated 7 days ago, created a post with more than 5 votes. For A: Trinity strand specific: RF or FR
Appreciated 5 weeks ago, created a post with more than 5 votes. For A: Trinity strand specific: RF or FR
Teacher 6 weeks ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Teacher 8 weeks ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Scholar 8 weeks ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Teacher 11 weeks ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Appreciated 3 months ago, created a post with more than 5 votes. For A: Trinity strand specific: RF or FR
Popular Question 3 months ago, created a question with more than 1,000 views. For Bioinformatician in genome annotation, Uppsala, Sweden
Prophet 4 months ago, created a post with more than 20 followers. For Orientation of PE reads a review of --fr --ff and --rf meanings
Student 4 months ago, asked a question with at least 3 up-votes. For Emboss seqret - problem conversion gff+fasta to EMBL
Teacher 7 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
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
Scholar 8 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
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
Appreciated 9 months ago, created a post with more than 5 votes. For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
Popular Question 9 months ago, created a question with more than 1,000 views. For Bioperl gff3 : How to print non gff3 feature as "###" using Bio::Tools::GFF
Scholar 10 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Teacher 11 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Scholar 11 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Scholar 12 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation
Teacher 13 months ago, created an answer with at least 3 up-votes. For A: Status of maker annotation

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