To filter out blast annotated reads on the basis of hits

Question

[faizansaleem1992]

Hello,

I have performed blast on my query file. Now i want to remove the sequences with no hits. How can I do that. ?

[Lars Juhl Jensen]

I am not sure I understand the problem. Is this not a simple matter of 1) parsing the BLAST output to identify which query sequences gave hits, and 2) extracting this subset of sequences from the query FASTA file?

[st.ph.n]

If you do a tab output -outfmt 6 for your blast, get the unique query ids with cut -f 1 blast_output.txt | sort | uniq > ids.txt. Then search Biostars, or code a way to keep sequences that match those ids, or remove the ones that don't.