User: Juke-34
Juke-34 • 1.2k
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Posts by Juke-34
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... Have a look [here][1] it has been already discussed
[1]: https://www.biostars.org/p/290651/ ...
written 9 weeks ago by
Juke-34 • 1.2k
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... You could use [this service][1] to look at the longest ORF in each exon.
For the first cds piece it's easy it is 0 (If you have your complete gene)
A good way would be to load your two genes in a genome browser allowing manual curation, and you merge your genes manually, then you download the resu ...
written 10 weeks ago by
Juke-34 • 1.2k
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Comment:
C: Genes, Isoforms, Proteins?
... I think you can find nice definitions on google, isn't it ?
Is there something particular that you are wondering ?
Have a look [here][1] it is a really nice documentation. I think you could find lot of things about isoforms (Alternative transcripts).
[1]: ftp://ftp.sanger.ac.uk/pub/project/havan ...
written 10 weeks ago by
Juke-34 • 1.2k
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... I implemented a parser to check, fix, pad any kind of gtf and gff to create complete and standardize gff3 format.
If you are interested you will find it in the github [NBISweden][1] repository. Follow the installation instruction [here][2], then the easiest is to use this script gxf_to_gff3.pl
If y ...
written 12 weeks ago by
Juke-34 • 1.2k
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... Why are you talking about gff3 ? Gff3 is a format with 9 columns.
Here is a 5 columns tabulated format. It is definitely not gff3 format.
...
written 12 weeks ago by
Juke-34 • 1.2k
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... I don’t know the use of those options but for sure it is fine without to determine the spicing sites.
For the extraction of spicing sites I have used fasta_domainExtractor_JD.pl from the [NBIS/GAAS][1] repository but it is not really adapted for what you want. You can get inspiration from this scr ...
written 3 months ago by
Juke-34 • 1.2k
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... You’re welcome. The problem is you provided a path but no file name. Instead of “/data/memona/hisat2-2.1.0/result/” do “/data/memona/hisat2-2.1.0/result/splice_sites.tsv” and it should be fine. ...
written 3 months ago by
Juke-34 • 1.2k
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... Hi blooming.daisy333,
It is explained in the [manual][1]. You have to use the option --novel-splicesite-outfile.
Be careful there is an error how left splice sites are reported as I mentioned [here][2].
[1]: https://ccb.jhu.edu/software/hisat2/manual.shtml
[2]: https://github.com/infphilo/his ...
written 3 months ago by
Juke-34 • 1.2k
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... Interesting... I have tried from two different location in Sweden without success....
both are in universities.... maybe a new firewall protection ...
Ok, I have tried using a vpn and now it is working !!
...
written 4 months ago by
Juke-34 • 1.2k
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... It is the third day I try without success... ftp 193.62.192.11 and ftp webin.ebi.ac.uk the same...
421 Service not available, remote server has closed connection
:( ...
written 4 months ago by
Juke-34 • 1.2k
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created an answer that has been accepted.
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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created an answer that was upvoted at least 5 times.
For A: Trinity strand specific: RF or FR
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For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
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8 months ago,
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For A: Where is it possible to submit annotated eukaryote genomes?
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For A: How to convert exon genomic coordinates to protein coordinates
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For A: Where is it possible to submit annotated eukaryote genomes?
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For C: How to manipulate a gff or gtf file manually?
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For A: Where is it possible to submit annotated eukaryote genomes?
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For A: Where is it possible to submit annotated eukaryote genomes?
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For A: Where is it possible to submit annotated eukaryote genomes?
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For A: How to convert exon genomic coordinates to protein coordinates
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For A: Extract fasta sequences from a large file using a list of names
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