User: Juke-34
Juke-34 • 3.2k
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- Sweden
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Posts by Juke-34
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... I have added `nseg` in bioconda, you can install it using bioconda now. ...
written 3 days ago by
Juke-34 • 3.2k
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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-34 • 3.2k
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... 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-34 • 3.2k
9
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11 follow
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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.
* ...
written 7 days ago by
Juke-34 • 3.2k
1
vote
3
answers
594
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3
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... 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-34 • 3.2k
0
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1
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... You can try with `agat_sp_manage_IDs.pl` from [AGAT][1]
[1]: https://github.com/NBISweden/AGAT ...
written 8 days ago by
Juke-34 • 3.2k
0
votes
1
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97
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1
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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-34 • 3.2k
1
vote
1
answer
131
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1
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... 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-34 • 3.2k
1
vote
2
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103
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2
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... it is available as conda package so you don't care it is in perl ;) ...
written 13 days ago by
Juke-34 • 3.2k
1
vote
2
answers
103
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2
answers
... 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-34 • 3.2k
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For A: Trinity strand specific: RF or FR
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For A: Trinity strand specific: RF or FR
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For A: How to convert exon genomic coordinates to protein coordinates
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For A: How to convert exon genomic coordinates to protein coordinates
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For Bioinformatician in genome annotation, Uppsala, Sweden
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For Orientation of PE reads a review of --fr --ff and --rf meanings
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For Emboss seqret - problem conversion gff+fasta to EMBL
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8 months ago,
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For A: How to convert exon genomic coordinates to protein coordinates
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For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
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For Bioperl gff3 : How to print non gff3 feature as "###" using Bio::Tools::GFF
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