User: Juke-34
Juke-34 • 1.1k
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Posts by Juke-34
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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 27 days ago by
Juke-34 • 1.1k
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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 27 days ago by
Juke-34 • 1.1k
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... to clone the repository:
git clone https://github.com/NBISweden/GAAS.git ...
written 4 weeks ago by
Juke-34 • 1.1k
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... There is no way to activate the option --gff3=yes of augustus ? That would be convenient...
Otherwise as mentioned in the other post (https://www.biostars.org/p/273355/#305301) you could use the gxf_to_gff3.pl script from here:
https://github.com/NBISweden/GAAS/tree/master/annotation/Tools/bin
but ...
written 4 weeks ago by
Juke-34 • 1.1k
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... Using the gxf_to_gff3.pl you will end up with a full and standardized gff3 file. If you wish to manipulate the attributes in a specific way you can have a try to the script called: gff3_sp_manage_attributes.pl ...
written 4 weeks ago by
Juke-34 • 1.1k
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... I'm pretty sure to have seen cross links to external databases when clicking on dbxref attributes in old version of webapollo.
I have installing the last version and I don't find any way to do so.
I have googled for hours without finding any convincing information.
Someone knows if it is still poss ...
written 5 weeks ago by
Juke-34 • 1.1k
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... I tried to submit an agp file to ENA but it didn't work. I had 4 times this error message:
> USER ERROR: "linkage_evidence" qualifier is allowed in "assembly_gap" feature
only when "gap_type" qualifier value equals to "within scaffold" or "repeat
within scaffold". [{FILE_NAME=xxx.agp.gz,
STAGE=V ...
written 5 weeks ago by
Juke-34 • 1.1k
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Comment:
C: Training Augustus for Maker
... It depends which version you use. Version 3 is like you said, version 1 is like I said, version 2 I don’t remember well but I think it was like version 1. ...
written 7 weeks ago by
Juke-34 • 1.1k
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... "that need a reference genome" Or "does not need" ?
Genome guided assembler : Cufflinks, Stringtie, bayesembler, etc... => sam/bam output
De-novo assembler : Trinity, Oases, SOAPdenovo-Trans, etc... => fasta output ...
written 7 weeks ago by
Juke-34 • 1.1k
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... Btw, at the end, how did it end up with EMBLmyGFF3 ? ...
written 9 weeks ago by
Juke-34 • 1.1k
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For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
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For C: How to manipulate a gff or gtf file manually?
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