To filter out blast annotated reads on the basis of hits
Hello,
I have performed blast on my query file. Now i want to remove the sequences with no hits. How can I do that. ?
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faizansaleem1992 •
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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?
If you do a tab output
-outfmt 6for your blast, get the unique query ids withcut -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.