standlone blast

[kulandaisamy]

how to get query coverage in blastp?

[skbrimer]

What you want in the outfmt option is qcovs, well at least its what I think you want.

[kulandaisamy]

i am running blastp in commandline.i didn't get query coverage results.how to got it?help me?

[GenoMax]

http://www.ncbi.nlm.nih.gov/books/NBK279690/

Check out the section on custom output formats.

Detailed explanation of command line output format options for blast: https://www.biostars.org/p/88944/

[skbrimer]

How about this. Can you provide some information on how you are trying to run the blast command line tool? Are you getting an error? If you can give any of us an idea of what you are doing and perhaps why it is not working for you then maybe someone can give you the answer you are looking for. If you do not feel that providing anything other than "please help me" I suggest you type "blast -help" in the command line and get to reading.

[kulandaisamy]

blastall -p blastp -i plas_3d7.fasta -d approved_target.fasta -m 8 > blas.tab

my output file contaiing only Query id, Subject id, % identity, alignment length, mismatches, gap openings, q. start, q. end, s. start, s. end, e-value, bit score.
i want query coverage results

[kulandaisamy]

how to use -qcovs flag in blastp?

[skbrimer]

blastall -p blastp -i plas_3d7.fasta -d approved_target.fasta -m 8 > blas.tab

I'm not sure how you would run the search in the older version of BLAST, NCBI recommends you download the new BLAST+ here is a link to a discussion https://www.biostars.org/p/9480/

I have only used the newer version so the line of code would look something like....

blastp -db nr -query plas_3d7.fasta -query_loc approved_target.fasta -out blas.tab -outfmt "6 qgi sgi qcovs" -remote

Or something to this effect, I'm not sure what the -d flag is on the blastall version of blast but hopefully this can get you pointed in the right direction.

[kulandaisamy]

ok.i tried to install blast+.but i didn't get it

[GenoMax]

What version of blast are you running?

$ blastp -version

[kulandaisamy]

blastp: 2.2.28+
Package: blast 2.2.28, build Jun 3 2013 11:32:37

[GenoMax]

You are running blast+. Not the latest (v. 2.2.30) but close enough. Use @skbrimer's suggestion for the command above.

[kulandaisamy]

ok..thnk you

[GenoMax]

Don't use the -remote option if you are using blast locally.

[kulandaisamy]

i tried but i didn't get it.give me some example.