How to know the query coverage
How to know the query coverage in the local blast output?
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Ram
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Stela Ribeiro •
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Stela Ribeiro •
2 answers
I quickly wrote a XSLT styleheet converting a blast+xml output to coverage data for each position of the query. The stylesheet is available at: https://github.com/lindenb/xslt-sandbox/blob/master/stylesheets/bio/ncbi/blast2coverage.xsl
Example:
$ xsltproc stylesheets/bio/ncbi/blast2coverage.xsl blastn.xml
#ID DEF POS LENGTH CONSENSUS DEPTH
gi|9626372|ref|NC_001422.1| Enterobacteria phage phiX174 sensu lato, complete genome 1 5386 GGGGGGGGGGGGGGGGGG 18
gi|9626372|ref|NC_001422.1| Enterobacteria phage phiX174 sensu lato, complete genome 2 5386 AAAAAAAAAAAAAAAAAA 18
gi|9626372|ref|NC_001422.1| Enterobacteria phage phiX174 sensu lato, complete genome 3 5386 GGGGGGGGGGGGGGGGGG 18
gi|9626372|ref|NC_001422.1| Enterobacteria phage phiX174 sensu lato, complete genome 4 5386 TTTTTTTTTTTTTTTTTT 18
gi|9626372|ref|NC_001422.1| Enterobacteria phage phiX174 sensu lato, complete genome 5 5386 TTTTTTTTTTTTTTTTTT 18
gi|9626372|ref|NC_001422.1| Enterobacteria phage phiX174 sensu lato, complete genome 6 5386 TTTTTTTTTTTTTTTTTT 18
gi|9626372|ref|NC_001422.1| Enterobacteria phage phiX174 sensu lato, complete genome 7 5386 TTTTTTTTTTTTTTTTTT 18
gi|9626372|ref|NC_001422.1| Enterobacteria phage phiX174 sensu lato, complete genome 8 5386 AAAAAAAAAAAAAAAAAA 18
gi|9626372|ref|NC_001422.1| Enterobacteria phage phiX174 sensu lato, complete genome 9 5386 TTTTTTTTTTTTTTTTTT 18
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Ram
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Pierre Lindenbaum
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Pierre Lindenbaum
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what's your input ? for each hit ?
It looks like a good alternative. Thank you very much, Pierre