User: El Niño

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El Niño10
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4 months ago
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Posts by El Niño

<prev • 16 results • page 1 of 2 • next >
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PlasmidSeeker error with a perl script
... Hi all, I have installed PlasmidSeeker on my Linux MInt 19 computer and now am trying to run it for the first time. I followed carefully this [workflow][1] But when I run the command perl plasmidseeker.pl -d db_w20/ -i TH19_1.filtered.fastq -b cereus-ATCC14579.fasta The terminal replied ...
perl plasmid permission-denied error written 11 weeks ago by El Niño10
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Bioinformatics tools for Plasmid detection
... Hi guys, Now I have a FASTA file which is the post-assembly sequence of a bacterial genome. Now I have some pre-annotated files that stated that there are 4 insecticidal genes in my sequence. I also know that normally, these genes are located on plasmid Surprisingly, when I uploaded my sequence to ...
plasmid tools short-read bioinformatics written 11 weeks ago by El Niño10
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PlasmidFinder installation error
... Hi guys, As I've got to find a way to detect possible plasmids in my whole genome, I've been working to install and use PlasmidFinder software on my Linux Mint 19 computer. So I follwowed this protocol [bitbucket.org/genomicepidemiology/plasmidfinder/src/master/][1] Then everything has been pla ...
installation plasmid genome annotation linux written 12 weeks ago by El Niño10
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Comment: C: An error while running Velvet
... Here is the script: https://github.com/dzerbino/velvet/blob/master/contrib/shuffleSequences_fasta/shuffleSequences_fastq.pl ...
written 3 months ago by El Niño10
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Comment: C: An error while running Velvet
... Thank you very much. That's exatly what I've been looking for. ...
written 3 months ago by El Niño10
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An error while running Velvet
... Hi guys, I am now running Velvet to do genome assembly, however at the very first step when I do shuffleSequences_fastq.pl file_1.fastq file_2.fastq merged.fastq I came across this error which reads: syntax error at shuffleSequences_fastq.pl line 10, near "<" Excessively long < ...
assembly written 3 months ago by El Niño10 • updated 7 weeks ago by Biostar ♦♦ 20
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Comment: C: Draw a genome map with CGView server?
... Yeah, should be that. But I still need to know why my data cannot generate a full genome map? Do you have any idea? ...
written 3 months ago by El Niño10
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Draw a genome map with CGView server?
... Hi everyone, I am a bioinformatics newbie. I was asked to draw a genome map of a strain of bacteria whose complete genome sequence has been worked out. However, when I put my .fasta file onto the website CGView server, it showed only the longest contig (~280KB) on the circular genome map, while in ...
cgview assembly genome map written 3 months ago by El Niño10
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Comment: C: VelvetOptimiser fails to operate
... Thank you so much. I will give SPAdes a shot now. ...
written 3 months ago by El Niño10
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How to know that your bacterial genome contain how many plasmids? And which genes are located on which plasmid or chromosome?
... Hi everyone, I am writing a genome announcement report. Upon reading those written and published previously by other authors, I noticed that they can state exactly which genes are located on which chromosomes and which plasmids. However, when I look at my annotation report, I cannot figure out the ...
genome annotation report written 3 months ago by El Niño10 • updated 11 weeks ago by Biostar ♦♦ 20

Latest awards to El Niño

Scholar 3 months ago, created an answer that has been accepted. For C: Problem with Velvet.

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