Entering edit mode
6.5 years ago
Ric
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430
Hi, I am running blastall -p blastn -i ${i} -d ${db} -F F -e 1e-10 -E -1 -v 20000 -b 20000 -a 1 -K 1 > output/${output}.blast and I just wondering how could I even further to reduce the output file size by e.g. reducing the number of hits?
Thank you in advance.
What would be the best values for -b and -v? I need to plot a circos plot.
It all depends of the question you ask (rather than the way of presenting the results)
I trying to plot synteny plots between a reference genome which has chromosomes and a new contig based assembly.
Then you should take only the best match I think