filtering blastx output file
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4 months ago
analyst ▴ 50

This is the standalone blast output header. I have to apply filtration w.r.t query coverage. Kindly guide which of the following columns represent query coverage.

Thanks

qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore

blastx query filtration coverage • 345 views
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I have visited this site already but query coverage is not given with default command or I am not able to get. I have to filter transcripts with coverage of target >80%. For that which column should I select for filtration?

qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore

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I have to remove transcripts with significant homology to known proteins (e.g., e-value <1e-10, coverage of target >80%, and identity >90%).

Should I use following command:

Note: Since I am not sure about coverage of target in the blastx output, I have written command below without adding that parameter temporarily.

awk '{ if ($3 <= 90 && $11 >= "1e-10") print $0}' blastx_output.txt > filtered.txt

the output contains evalue with 2e-n to onwards. Is it right or should I use $11 <= "1e-10"

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Which filtering option should I use to get novel transcripts?

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