Hi,
I am using a local install of blastn to look for hits to a custom database from a bunch of short reads. In my final output file, I really only care about reads that found a 'hit' and so want to filter out all reads with 'no hits'. My strategy is as follows:
Read 1
Read 2
.
.
Read X
-> Put into one big FASTA file
-> Run blastn against the custom database
-> Save to file reads with hits only.
Right now (the standard blast output) would be:
Read 1 -> hit 1
Read 2 -> no hit
. -> no hit
. -> no hit
Read X -> hit X
But I want my output to only show:
Read 1 -> hit 1
Read x -> hit X
Since I have many reads and very few hits, my output file very rapidly gets filled with all the 'no hits' reads slowing down the whole process. Is there a way to filter my output directly via the command line, or do I need to build a script to do this?
Thanks in advance,
Kristian
I am using a local install of blastn to look for hits to a custom database from a bunch of short reads. In my final output file, I really only care about reads that found a 'hit' and so want to filter out all reads with 'no hits'. My strategy is as follows:
Read 1
Read 2
.
.
Read X
-> Put into one big FASTA file
-> Run blastn against the custom database
-> Save to file reads with hits only.
Right now (the standard blast output) would be:
Read 1 -> hit 1
Read 2 -> no hit
. -> no hit
. -> no hit
Read X -> hit X
But I want my output to only show:
Read 1 -> hit 1
Read x -> hit X
Since I have many reads and very few hits, my output file very rapidly gets filled with all the 'no hits' reads slowing down the whole process. Is there a way to filter my output directly via the command line, or do I need to build a script to do this?
Thanks in advance,
Kristian
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