Convert BLAST NC_ labels to chromosome label
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4.3 years ago
DVA ▴ 550

I was trying to use BLAST output (hit table csv) files for some downstream analysis, but found that this kind of output does not have a simple chromosome number on it. It looks like:

aSU,gi|568815584|ref|NC_000014.9|,aSU,NC_000014.9,100.000,29,0,0,32,60,105863255,105863227,7.13e-06,54.7
aSU,gi|528476665|ref|NC_018913.2|,aSU,NC_018913.2,95.833,24,0,1,29,51,32271236,32271213,0.72,38.1

I do recall that the "NC_" label may stand for chromosome, but I cannot find a summary table for all the cases on NCBI website. Any help is appreciated.

blast • 1.0k views
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4.3 years ago
mastal511 ★ 2.1k

The NC_ identifiers are RefSeq chromosome identifiers.

See this previous post, How to get the chromosome numbers from RefSeq accession IDs?.

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Thank you @mastal551

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