filtering blastx output file
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
• 1,173 views
•
link
0 answers
No answers yet.
Log in to answer this question.
Column descriptions found here: https://www.metagenomics.wiki/tools/blast/blastn-output-format-6
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?
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.
the output contains evalue with 2e-n to onwards. Is it right or should I use $11 <= "1e-10"
Which filtering option should I use to get novel transcripts?