User: El Niño

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El Niño10
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Posts by El Niño

<prev • 13 results • page 1 of 2 • next >
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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 5 days 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 5 days 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 5 days ago by El Niño10 • updated 5 days ago by lieven.sterck5.2k
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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 20 days 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 20 days 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 20 days 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 21 days ago by El Niño10
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Comment: C: VelvetOptimiser fails to operate
... In fact, it was not me who did the genome assembly but that was done by another lab. Based on their data, this genome contains 630,302,822 bp with 6,240,622 reads. Genome assembly gives 201 contigs with total number of bases of 5,830,249. They did paired-end sequencing and what I got was fna, gbk, g ...
written 21 days ago by El Niño10
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Comment: C: VelvetOptimiser fails to operate
... In fact, my genome was assembled using SOAPdenovo (1st version) and after that the problem is there are two many contigs and too many gaps that I need to link them together for a single circular genome so that I can draw a genome map. Do you have any idea how to do this? Thank you a bunch in advanc ...
written 21 days ago by El Niño10
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Comment: C: VelvetOptimiser fails to operate
... Hi ATpoint, I Googled for this whole problem and it turned out what I need was install Bioperl. So I follow [this tutorial][1] and got stuck at the last step, which I pasted all the error details on my post. Best regards, [1]: http://etutorials.org/Programming/perl+bioinformatics/Part+II+Perl+ ...
written 25 days ago by El Niño10

Latest awards to El Niño

Scholar 25 days ago, created an answer that has been accepted. For C: Problem with Velvet.

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