User: jf

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jf0
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Posts by jf

<prev • 7 results • page 1 of 1 • next >
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converting vcf to genepop with pgdspider for lositan
... Hello, I am using the output vcf from tassel uneak as the input vcf for pgdspider. Then I am trying to use pgd spider to convert the file to genepop for lositan to find outlier snps. In pgd spider I am inputting a population definitions file like: Fe-36 TW_1 Fe-51 TW_1 Fe-76 TW_1 there are 4 popu ...
locitan genepop pgdspider written 9 days ago by jf0
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Comment: C: local blastn against one subgroup of species
... Interesting idea, if I run "blastn -seqidlist" I get this error: "Error: Argument "-seqidlist". Value is missing". I need to add a file path after the option. My question is do I need the file to include "NC_" or "NG_"?, I think the available literature supports the idea of running -gilist instead b ...
written 14 days ago by jf0
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local blastn against one subgroup of species
... Hello, thanks to the great resource of this forum I was able to blastn a .fa file against a local blast database. The issue I am having is that the pipeline is blasting against every available sequence in the database. Even with the option: "-qcov_hsp_perc 0.95" I am getting good coverage but specie ...
blastn written 15 days ago by jf0
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Comment: C: local blast on ubuntu 17.04 using refseq_genomic
... Thank you I got it to run based on your recommendations ...
written 28 days ago by jf0
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Comment: C: local blast on ubuntu 17.04 using refseq_genomic
... genomax, I just ran: update_blastdb refseq_genomic and got: Connected to NCBI Downloading refseq_genomic (291 volumes) ... and all volumes were up to date, I do have the .nal file in my db directory I then gunzip every .tar.gz file <- do I have to extract the .tar files? Then run blast from the ...
written 4 weeks ago by jf0
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Comment: C: local blast on ubuntu 17.04 using refseq_genomic
... yamule, thank you for catching that oversight on my part, that did fix the issue. ...
written 4 weeks ago by jf0
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local blast on ubuntu 17.04 using refseq_genomic
... Hello I am trying to run local blast on ubuntu 17.04. I have blast installed: ncbi-blast+ is already the newest version (2.6.0-1). then export BLASTDB=path/to/blastdb/folder Then cd into blastdb and I ran: update_blastdb refseq_genomic to download all 289 files. Now I want to be able to scre ...
blast refseq written 4 weeks ago by jf0

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