start and stop position of mapping in Blast

[Navy1991]

I used makeblastdb to search many short fasta sequences in a known organism. I successfully completed this step and got the mappings. My question is

1. how can I get the start and stop coordinate ?

for eg

Query 1 AATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGATAtttttattt 60
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct 1765181 AATATAGGTGGTACCACGGAATATCCGTCCTATTTGTATATAGGATGGATATTTTTATTT 1765122

Query 61 ttttAGGAGGTATAGCAAATGG 82
||||||||||||||||||||||
Sbjct 1765121 TTTTAGGAGGTATAGCAAATGG 1765100



How to get 1765100 and 1765181 from a text file with many mappings like this. I would also like to count the number of mappings or query sequences?

[wolma]

Well, you need a script to parse the results file.
If you're hoping to get one though, you need to provide a full example of a results file, not just a random excerpt from it.

[mastal]

If you are running blast from the commandline, type 'blastn -help',
and you will get a help page.

It sounds like what you need is blast's tabular output, outfmt6 or outfmt7,
and the parameters to give you the alignment coordinates would be qstart, qend, sstart, send.

See the blast manual,

https://www.ncbi.nlm.nih.gov/books/NBK1763/

[Navy1991]

Answer

blastn -query some.fa -db some.fa -outfmt 6 | awk '{print $9 "\t" $10}'