Including "no significant hits" in output of local blastn searches

Question

[newol210]

This is my my blastn command that uses '/ordered.fasta' as a query and searched the nt database for matches:

blastn -query ./ordered.fasta -db nt -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore salltitles" -max_target_seqs 1 -num_threads 20 -evalue 1e-5 -out ./blast_searches/De_novo_edgeR_sig_DEGs.txt

The output file is good, but I'm wondering if anyone knows if there is a way to write out "no significant hits" (or similar) for sequences that didn't have a good match? These sequences could be important so I want them to be included in my final output file, so I can investigate them later using other databases.

Thanks in advance!

Answer 1

[Mensur Dlakic]

Sequence IDs not listed in the output file will not have significant hits, and BLAST is not meant to report them in tabular format. If you run this in pairwise mode, which is considerably more difficult to parse, sequences without any matches will have a "No significant matches" in the output.

This command will give you all the sequences that have matches:

awk '{print $1}' blast_searches/De_novo_edgeR_sig_DEGs.txt | sort -u > matches.txt

There is an explanation how to "subtract" these sequences from your original file, which should give you a FASTA file of sequences that didn't match anything.

[newol210]

Thats a bummer. Thanks for your help though!

Answer 2

[lieven.sterck]

As Mensur Dlakic correclty points out, there is no direct way to do this .

However there is a quite neat workaround to achieve this. Besides the outformat 6 you can also go for the tabular outformat 7 (==tabular with comment lines) which is nearly identical to the 6 with the only difference that it includes a few header lines per search entry. If a query has no significant hits, you can spot this as header lines without any hits underneath it moreover one of the comment lines will indicate '0 hits found'. (the hit part itself is identical to the outformat 6)

It is not as neat as to see it nicely printed in the tabular fields but it is workable.