Standalone blast: how to display only results with positive number of hits ?

Question

[lordbleys]

Hi!

Here is my problem: I have a list of sequences (reads in fasta format) from a NGS experiment, and I want to identify some specific sequences in this list and count the number of occurrences they occur. The sequences I am looking for are grouped into a database (another fasta file).

I use a local standalone blast the following way:

makeblastdb -in database.fasta -out database -dbtype nucl
blastn -db database -query ngs_reads.fasta -out results.out

The problem is that the output file displays all the input sequences (several millions in my case), and only a handful of them actually score hits in the database. As a results I have a very impractical file to read until I find the results I am looking for.

I tried using the -outfmt option, but to no avail:

-outfmt "7 qacc sacc evalue length nident"

Also, the database is pretty big also, so inverting db/query doesn't really help (already tried).

My question is : is there a way to display only the query sequences for which the number of hits is > or = to 1 in the blastn output?

Any help would be most welcome! :)

[5heikki]

Why did you try outfmt 7 in particular? Have you read the manual/even checked the -help option? There are multiple suitable outfmts for you..

[GenoMax]

See this thread for some discussion about this: http://seqanswers.com/forums/showthread.php?t=14498

[lordbleys]

Thanks !

I tried outfmt 7 because of the formatting and the options, I didn't realize the "comment line" was my problem. Indeed very simply with the outfmt 6 it works perfectly.

[iraun]

Have you try to specify a value for evalue parameter?