User: Juke-34

gravatar for Juke-34
Juke-341.1k
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Posts by Juke-34

<prev • 215 results • page 1 of 22 • next >
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Comment: C: Uploading data files to Webin upload area under Linux
... 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-341.1k
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Comment: C: Uploading data files to Webin upload area under Linux
... 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-341.1k
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Comment: C: How can I use rewrite the contents of the attribute column in a gff output from
... to clone the repository: git clone https://github.com/NBISweden/GAAS.git ...
written 4 weeks ago by Juke-341.1k
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Comment: C: How can I use rewrite the contents of the attribute column in a gff output from
... 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-341.1k
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Comment: C: GFF3 file incompatibilities (source: BRAD)
... 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-341.1k
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Webapollo - dbxref - cross links to external databases
... 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 ...
genome written 5 weeks ago by Juke-341.1k
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error in AGP file
... 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 ...
assembly written 5 weeks ago by Juke-341.1k
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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-341.1k
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Comment: C: alignment software that does not require a reference genome
... "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-341.1k
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Comment: C: GFF to TBL file conversion for annotation submission
... Btw, at the end, how did it end up with EMBLmyGFF3 ? ...
written 9 weeks ago by Juke-341.1k

Latest awards to Juke-34

Good Answer 5 weeks ago, created an answer that was upvoted at least 5 times. For A: Trinity strand specific: RF or FR
Appreciated 10 weeks ago, created a post with more than 5 votes. For A: Script for getting summary statistic of any genome using GTF or GFF3 ?
Supporter 4 months ago, voted at least 25 times.
Teacher 4 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Scholar 6 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Teacher 6 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Commentator 7 months ago, created a comment with at least 3 up-votes. For C: How to manipulate a gff or gtf file manually?
Guru 7 months ago, received more than 100 upvotes.
Appreciated 14 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 14 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Popular Question 14 months ago, created a question with more than 1,000 views. For Emboss seqret - problem conversion gff+fasta to EMBL
Teacher 17 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Teacher 18 months ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Centurion 22 months ago, created 100 posts.
Scholar 22 months ago, created an answer that has been accepted. For A: How to convert exon genomic coordinates to protein coordinates
Scholar 2.3 years ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names
Teacher 2.4 years ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Scholar 2.6 years ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names
Teacher 2.6 years ago, created an answer with at least 3 up-votes. For A: Where is it possible to submit annotated eukaryote genomes?
Scholar 3.0 years ago, created an answer that has been accepted. For A: Extract fasta sequences from a large file using a list of names

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