User: User 6228

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User 6228100
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100
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New User
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Last seen:
7 years, 7 months ago
Joined:
7 years, 10 months ago
Email:
u2262

Posts by User 6228

<prev • 8 results • page 1 of 1 • next >
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Blast_Formatter: How To Choose Which Database To Read From?
... Hi, I am attempting to use the blast_formatter included with Blast+ 2.2.24 to convert a blast archive file to xml format. However, I get this error message when I run the command: BLAST Database error: Nucleotide BLAST database 'beij' does not exist in the NCBI servers Here is the command I'm run ...
blast written 7.8 years ago by User 6228100 • updated 7.8 years ago by ALchEmiXt1.9k
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6 follow
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Blastn - Program Runs Indefinitely When Generating Xml Formatted Output
... I am running blastn on some nucleotide data, and it seems to run indefinitely when I generate XML output. The jobs take ~15 minutes when generating either the default format or tab delimited, but when I choose XML format each job maxes out the 3 hour cap I have set on it. I find it hard to believe ...
nucleotide blast written 7.8 years ago by User 6228100 • updated 2.5 years ago by Biostar ♦♦ 20
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Answer: A: How Can I Align My 454 Reads To A Reference Sequence And Generate A Recruitment
... I ended up borrowing (with permission) the Javascript from this site: http://weizhong-lab.ucsd.edu/frv/, then I wrote a tiny php backend that parses Blast and FR-Hit files and sends the data to the Javascript plotter in the right format. It works very well on my system, but you will have to apply a ...
written 7.8 years ago by User 6228100 • updated 7.1 years ago by Istvan Albert ♦♦ 80k
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Comment: C: What Is The Difference Between 'Fragment Recruitment' And 'Aligning Reads To A R
... From Aleksandr's answer, I understand that 'fragment recruitment' applies specifically to metagenomic data and finding which species are represented, while 'aligning reads' applies to a broader range of read to reference sequence comparisons (for example, measuring how well a subset of mouse DNA is ...
written 7.9 years ago by User 6228100
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Comment: C: What Is The Difference Between 'Fragment Recruitment' And 'Aligning Reads To A R
... Perfect, thank you. Could you explain in more detail what you mean about 'more culture around fragment recruitment'? ...
written 7.9 years ago by User 6228100
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Comment: C: How Can I Align My 454 Reads To A Reference Sequence And Generate A Recruitment
... I can align it with a reference sequence (blast, fr-hit, etc) but I need something to plot it. I will take a look at R. ...
written 7.9 years ago by User 6228100
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What Is The Difference Between 'Fragment Recruitment' And 'Aligning Reads To A Reference Sequence'?
... I have to perform 'fragment recruitment' on my metagenomic reads to generate plots of the percentage identity in the reference sequences. From what I can tell, fragment recruitment just amounts to aligning the reads to a reference sequence. However I believe there are subtle differences in what ...
reference blast written 7.9 years ago by User 6228100 • updated 7.9 years ago by Aleksandr Levchuk3.1k
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How Can I Align My 454 Reads To A Reference Sequence And Generate A Recruitment Plot?
... I'd like to align my trimmed 454 metagenomic reads to a reference sequence and generate plots of the coverage / percent identity / recruitment. Both the reads file and the reference file are in fasta format. I don't have access to the original .sff files from the 454 sequencer. I think consed can ...
fasta written 7.9 years ago by User 6228100 • updated 22 months ago by Biostar ♦♦ 20

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