User: asjo

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asjo120
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6 years, 1 month ago
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Posts by asjo

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Comment: C: State Of The Art In Base-Calling?
... I was thinking of "classical"(?) Sanger sequencing. Sorry, I should have specified that. I have updated the question and tags accordingly. ...
written 6.1 years ago by asjo120
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State Of The Art In Base-Calling?
... What is state-of-the art in base-calling for Sanger sequencing these days? Does Phred+Phrap still reign supreme? Do newer or better programs exist? What are people using? Any Free (open source) implementations? References to algorithms, implementations, or papers would be great. ...
sanger calling sequencing written 6.1 years ago by asjo120 • updated 6.1 years ago by Gabriel R.2.6k
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Comment: C: Why Should I Use Galaxy ?
... lynx predates curl by ~5 years :-) ...
written 6.7 years ago by asjo120
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Answer: A: Newick 2 Json Converter (Preferably In Perl)
... Here is an attempt, with the caveat that your example is really complicated, and that you haven't really defined what the JSON result should look like: #!/usr/bin/perl use strict; use warnings; use Bio::Phylo::IO; use JSON; my $forest=Bio::Phylo::IO->parse(-file=>"example.newick", -format= ...
written 6.7 years ago by asjo120
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Comment: C: Newick 2 Json Converter (Preferably In Perl)
... How do you expect the JSON to look? ...
written 6.7 years ago by asjo120
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Answer: A: Postgresql: Select Only Taxa Which Are Children Of A Given Taxon Using Parent Ta
... Using the same example data as in my answer using connectby(), here is a solution using commont table expressions instead. All the results under Bacteria: taxonomy=# SELECT * FROM result JOIN (WITH RECURSIVE relevant_taxonomy AS (SELECT taxon_id FROM taxonomy WHERE taxon_id=2 UNION ALL SELECT taxono ...
written 6.9 years ago by asjo120
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Answer: A: Postgresql: Select Only Taxa Which Are Children Of A Given Taxon Using Parent Ta
... One solution is to use the connectby() function from the tablefunc contrib extension. In PostgreSQL 9.1+ you install it simply by going CREATE EXTENSION tablefunc; With a little example taxonomy tree looking like this: taxonomy=# SELECT * FROM taxonomy ORDER BY id; id | taxon_id | parent_taxon_id | ...
written 6.9 years ago by asjo120
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Comment: C: Postgresql: Select Only Taxa Which Are Children Of A Given Taxon Using Parent Ta
... Why does the blast result table have both a tax_id and a taxonomy_id column? Ah, taxonomy_id refers to taxonomy(id) while tax_id refers to taxonomy(taxon_id). Having redundancy like this is not the best idea. ...
written 6.9 years ago by asjo120

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