User: anicet.ebou
anicet.ebou • 160
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Posts by anicet.ebou
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Answer:
A: Install BLAST in ubuntu
... This answer should help you.
1.Retrieve blast executables (if not already done) in the terminal:
1.1 Download the executables with the command:
wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/LATEST/ncbi-blast-2.10.0+-x64-linux.tar.gz
1.2 Decompress the archive and rename it:
t ...
written 4 months ago by
anicet.ebou • 160
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... Hello, I'm not a daily vst user but I would recommend you to take a look at this [paper][1], it will help you take decision on which method to use.
[1]: https://microbiomejournal.biomedcentral.com/articles/10.1186/s40168-017-0237-y ...
written 4 months ago by
anicet.ebou • 160
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... Hello,
I am wondering if the reads obtained following the [Earth Microbiome Project for 16S sequencing](http://press.igsb.anl.gov/earthmicrobiome/protocols-and-standards/16s/) protocol comes with primers already removed or not? ...
written 9 months ago by
anicet.ebou • 160
• updated
8 months ago by
Biostar ♦♦ 20
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... Yes, if the filename format is like FILENAME_XXX.fastq then I'm almost sure that it is a single-end reads file. ...
written 10 months ago by
anicet.ebou • 160
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... Do your internet connection use a proxy? ...
written 10 months ago by
anicet.ebou • 160
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... Generally, if the reads are paired-end data, the filename should be something like FILENAME_XXX_R1.fastq and FILENAME_XXX_R2.fastq and otherwise, for single-end, it should be something like FILENAME_XXX.fastq. Do the name of your file is formated in such a way? ...
written 10 months ago by
anicet.ebou • 160
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Comment:
C: Fastq-dump does not work
... Please can you add the command you try to execute ? ...
written 10 months ago by
anicet.ebou • 160
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... Ok I forward you a software recommendation but I didn't use it by myself: MEGAN6, Microbiome analysis using a single application. http://ab.inf.uni-tuebingen.de/software/megan6/. Hope It will help you. ...
written 19 months ago by
anicet.ebou • 160
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... I don't know a way to have BlastKOALA installed locally. But I know another way to have KO annotation: KAAS automatic server [here][1]. And KAAS have a standalone version for Linux and Mac OS available at [here][2].
[1]: https://www.genome.jp/tools/kaas/
[2]: ftp://ftp.kuicr.kyoto-u.ac.jp/mori ...
written 19 months ago by
anicet.ebou • 160
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... I think this answer can help you figure out how to do the job. https://www.biostars.org/p/232945/ ...
written 19 months ago by
anicet.ebou • 160
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