I am currently using blastn. I can use the perc_identity parameter to set my percent identity cutoff to 80%. However, I also want to set an alignment length / query coverage cutoff of 80%. Is this possible?
I am also using tblasn which does not even have a perc_identity parameter.
In the absence of these filters is there some way to easily analyze a large blast output? For example I did a tblastn on 100 isolates looking for hits of a specific gene. Since tblastn does not have a percent identity filter or alignment length filter I have lots of hits above and below my threshold of 80%. Is there a way for me to quickly check how many hits I have above my threshold without manually checking the values for each hit in my blast results?
to get query coverage with