User: dp

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dp30
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4 days, 19 hours ago
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2 years, 1 month ago
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d*********@yahoo.ca

Posts by dp

<prev • 20 results • page 1 of 2 • next >
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Answer: A: blastp multiple local databases error
... I learned that all dbs must have the same value of use_seqids. Since nr was created using use_seqids, this worked once I re-created my db with it as well. ...
written 4 days ago by dp30
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Comment: C: blastp multiple local databases error
... OK good idea. Thanks! ...
written 5 days ago by dp30
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Comment: C: blastp multiple local databases error
... No - I just downloaded the blast+ v2.10 executables for linux ...
written 6 days ago by dp30
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Comment: C: blastp multiple local databases error
... Thanks! Everything should be v5 - I am using BLAST+ 2.10 and fresh nr. I get the same error using an alias file as you suggested ...
written 6 days ago by dp30
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Comment: C: blastp multiple local databases error
... Thanks! I will try that now. Do you know why the -db option doesn't work? [This section of the user manual][1] says: "BLAST has been able to search multiple databases since 1997. The databases can be listed after the “-db” argument or in an alias file" [1]: https://www.ncbi.nlm.nih.gov/books/NB ...
written 6 days ago by dp30
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blastp multiple local databases error
... Hi I've come across an error/bug using blastp with multiple local databases. I am blasting against a local copy of nr and an in house database. When I blast against each separately there is no problem, but when I use the option: -db '/path/to/mydb /path/to/nr' I get the following error: `BLAS ...
blastp blast multiple databases ncbi blast written 6 days ago by dp30
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How to get reference genome sequence given species name
... Hi I have a list of bacterial species and would like to programmatically download all of their reference genomes. The list includes only the names of the species. eg: Actinomyces_viscosus Corynebacterium_matruchotii : : etc etc Is there an easy way to do this? Thanks! ...
genome reference sequences written 26 days ago by dp30 • updated 26 days ago by svp60
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Clean co-assembly using assembly
... Is there a tool to automatically clean up a co-assembly of multiple metagenomic samples using individual assemblies of each sample? Or at least score each co-assembled contig with a likelihood of being genuine/chimeric based on the contigs in the individual assemblies? Thanks! ...
assembly metgenomics co-assembly written 9 weeks ago by dp30
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automatically get description of genes found by blast
... Hi I BLASTed genes predicted from metagenomic contigs against nr/nt. For each match I get the accession and coordinates of the match in the reference. How can I programmatically get the annotations of these matches. For example, if I use the ncbi blast server I can go to each gene with matches, go ...
gene annotation metagenome blast written 3 months ago by dp30
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Using GFA assembly graphs
... Hi I have been using the assembly graphs output in fastg format by (meta-)SPAdes and megaHIT. They are relatively easy to parse and manipulate in Python - for example, to load the graph structure using networkX and associate sequences, sequence lengths, and depths with the nodes in the graph. I'm ...
assembly gfa written 3 months ago by dp30

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Popular Question 9 weeks ago, created a question with more than 1,000 views. For Reverse complements in BWA

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