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This might work:
Code:
makeblastdb -in $(cat Strains/*.fasta) -dbtype 'nucl' -out db/stec_samples
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savetherhino.org -
BLAST does not like this kind of command, where the second FASTA file is considered to be a positional argument:Originally posted by poudap View Post
From past experimentation, I know it will work if you quote the list of filenames making them space separated (filenames with spaces are a problem):Code:makeblastdb -in Strains/example1.fasta Strains/example2.fasta -dbtype nucl -out db/stec_samples
Code:makeblastdb -in "Strains/example1.fasta Strains/example2.fasta" -dbtype nucl -out db/stec_samples
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Unfortunately the $(cat Strains/*.fasta) command did not work.
The command space seperated also gave error:
BLAST options error: File Sample_no2.fasta does not exist.Comment
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The simple brute force solution is make a single merged FASTA file (e.g. using the cat command), and then build a BLAST database out of that.Comment
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Dear all, In creating a local blast database, I downloaded fasta files from ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ and http://www.ncbi.nlm.nih.gov/sites/nu...=%22Viruses%22[PORG]+AND+srcdb_refseq[PROP]. The former appeared larger than the latter, which of them is better? Do both both contain nr sequences? are they different?
ThanksComment
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I think a separate thread would be a good idea for this question. See also http://blastedbio.blogspot.co.uk/201...-chimeras.html and http://www.ncbi.nlm.nih.gov/pubmed/?term=25428358Originally posted by kaps View PostComment
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Hello Maubp,Originally posted by maubp View Post
Thanks for the blog links. i have also created a seperate thread as advised. its now called fasta files from NCBIComment
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Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.07-01-2026, 11:43 AM
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I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.
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