Blastn output format 6

See also:

• Blast documentation
• Blast on Metagenomics Wiki
• blastn -help and check -outfmt formatting option

Prepare the database

Only needed if reference sequences are going to be used frequently

makeblastdb \
  -in myRefSeqs.fasta \
  -out "My/Folder/myRefSeqs_blastdb" \
  -dbtype "nucl" \
  --parse_seqids \
  -logfile My/Folder/logFile.log

Run Blast

-num_alignment default is 250. Modify it if more alignments are expected
-outfmt sets the output format

blastn \
  -task megablast \
  -query InputSequence.fasta \
  -db "My/Folder/myRefSeqss_blastdb" \
  -out My/Output/Folder/InputSeq_vs_RefSeqs.res \
  -outfmt 6 \
  -num_alignments 10000000

Run blast with 2 fasta sequences:

blastn \
  -query genes.fasta \
  -subject genome.fasta \
  -outfmt 6

Default value for -outfmt 6 corresponds to -outfmt "6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore"

Output

Column headers:
qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore
In R:

c("qseqid","sseqid", "pident", "length", 
  "mismatch", "gapopen", "qstart", "qend", 
  "sstart", "send", "evalue", "bitscore")

Col	name	Description
1.	qseqid	query (e.g., unknown gene) sequence id
2.	sseqid	subject (e.g., reference genome) sequence id
3.	pident	percentage of identical matches
4.	length	alignment length (sequence overlap)
5.	mismatch	number of mismatches
6.	gapopen	number of gap openings
7.	qstart	start of alignment in query
8.	qend	end of alignment in query
9.	sstart	start of alignment in subject
10.	send	end of alignment in subject
11.	evalue	expect value
12.	bitscore	bit score