Hi all,
I am running blast+/v2.8.1 as follow:
blastn -db mydatabase_db -query mysample.fa -out resultsblast -evalue 1e-6 -perc_identity 90 -max_target_seqs 10 -num_threads 8 -outfmt 7
See the output below.
How can I see a list of true hits found?
# BLASTN 2.8.1+
# Query:
# Database: mydatabase_db
# 0 hits found
# BLASTN 2.8.1+
# Query: CLocus_20_Sample_32_Locus_20_Allele_0 [QSI_A1]
# Database: mydatabase_db
# 0 hits found
# BLASTN 2.8.1+
# Query: CLocus_20_Sample_32_Locus_20_Allele_1 [QSI_A1]
# Database: mydatabase_db
# 0 hits found
# BLASTN 2.8.1+
# Query: CLocus_20_Sample_33_Locus_20_Allele_0 [QSI_A2]
# Database: mydatabase_db
# 0 hits found
# BLASTN 2.8.1+
# Query: CLocus_20_Sample_33_Locus_20_Allele_1 [QSI_A2]
# Database: mydatabase_db
# 0 hits found
# BLASTN 2.8.1+
# Query: CLocus_20_Sample_34_Locus_20_Allele_0 [QSI_A3]
# Database: mydatabase_db
# 0 hits found
# BLASTN 2.8.1+
I guess you are using
-outfmt 7
to see queries that don't have hits because otherwise you can simply use-outfmt 6
to only get results for queries that have hits.