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How to get 1 top hit only for each query in blastx

I am running blastx using the following command:

blastx -query CDS.fa -db local_path_nr -num_threads 36 -evalue 1e-5 -outfmt 6 -max_target_seqs 1 -out CDS_blast.txt

I aim to get one hit for each query only but there are still, say 2-3 hits, per query occasionally. How do I save the top hit only? I know this can be done post-blast, but can I simply achieve it while running blast? Thanks!

blast rna-seq blastx
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updated by Fatima Fatima • written by 2822462298 • 2822462298

It should be easy for you to parse the output file such that only the top hit is retained.

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written by Kevin Blighe Kevin Blighe

I guess this command does not apply to blastx

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written by 2822462298 • 2822462298

2 answers

The max_hsps never really worked properly, they have some explanation for this if I recall. You can use sort to do that:

sort -k1,1 -k11,11g CDS_blast.txt | sort --merge -u  -k1,1

This will sort by query sequence and p-value (assuming default format 6 output), then will select the first result (lowest p-value) for each query

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written by Asaf Asaf

Thanks Asaf, yeh I agree the built-in option does not work properly.

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written by 2822462298 • 2822462298

Have you tried this option: 

-num_alignments 1

You can also check other options using: 

blastx --help
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written by Fatima Fatima

Hi Fatima, I tried it and I got the same result...

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written by 2822462298 • 2822462298

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