Blastn in galaxy
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8 weeks ago

Dear colleagues, I am conducting RNA-seq analysis for discovering viruses associated with plants. My pipeline is trimming data, mapping with the host genome and assemble the unmapped reads. Application of the BLASTn in galaxy server to the contigs obtained with local downloaded plant viruses genomes from NCBI. However, I am facing a tedious issue related to the match contigs in the output table where I get the accession number only of the viruses that match my contigs and this is tedious because I need to take the accession number to the NCBI to figure out the virus name for each one. Thus, could anyone help me to overcome this issue, please.

using galaxy Blastn in • 296 views
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your question is a bit unclear, are you asking about matching an NCBI accession number to a scientific name?

show some parts of your file

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The output table

Thanks for your response and please see below the table and I have determined the accession number column with red colour that I need it to be the name of viruses, not their accession number only.

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Thank you so much for your attention and response. I have fixed the problem

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8 weeks ago
GenoMax 102k

with local downloaded plant viruses genomes from NCBI

Did you create a custom database from downloaded genomes? If you simply download the genomes from NCBI, did you choose Parse the sequence identifiers when you created your blast database using makeblastdb? If not you should do that. Then your tabular blastn output in galaxy should contain the name of the hit/subject in column 25 of the output.

You could also choose Tabular (select which columns) output option and customize the table per your desire.

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I am high appreciated you. I have overcome the problematic issue.

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