Comments (2)
Hi Jubin
I am really sorry for my late reply. I had many exams a few days ago.
I appreciate your interest in testing this tool.
Unfortunately, I haven't included the query/hit coverage parameter in the mining algorithm. However, you can still add it when you run the blastn program.
For example:
In the "full_pipeline" mode, you can use -bp option and specify the query/hit coverage. e.g., -bp "-qcov_hsp_perc 80"
$blastMining full_pipeline
-i ASV.fasta
-o vote_pipe
-bp "-db nt -max_target_seqs 10 -num_threads 5 -qcov_hsp_perc 80"
-m vote
-e 0.001
-txl 99,97,95,90,85,80,75
-n 10
-sm 'Sample'
-j 8
-p lca_method
-kp
-rm
Best regards
Khoiri
from blastmining.
No worries @NuruddinKhoiry and many thanks for your response. Sure, I can just stick to the coverage parameter in blastn
from blastmining.
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