blast alignemnt query coverage

Question

[sharmatina189059]

Can anyone tell me the error in this command. I want to get full query coverage also with my seq. alignment and when I am using qcovs it is showing error.

blastn -db 17978_old_complete_genome -query 17978new_ol_genes.fasta -perc_identity 90 -evalue 0.0001 -qcovs -outfmt 6  > complete_genome_0.0001_oneline_output_qcovs

[Karma]

Just try the same command with quotes The command string needs these quotes, such that the command line looks like:

blastn -outfmt "6 qcovs" ...

[sharmatina189059]

Thanks ..it works but which coloumn gives query coverage

[Karma]

why don't you upload your results.. at-least first 10 lines

[GenoMax]

Output should be in the same order as what you specified in -outfmt 6 "sseqid qseq qcovs sseq" gives you

gi|672239066|ref|NR_125655.1|   AACTGACAGTTTTAGAAACAGGACT   2   AATTGACAGTTTTAGAAATAGAACT
gi|631253076|ref|NR_114274.1|   AACTGACAGTTTTAGAAACAGGACT   2   AATTGACAGTTTTAGAAATAGAACT
gi|636560310|ref|NR_116370.1|   AACTGACAGTTTTAGAAACAGGACT   2   AATTGACAGTTTTAGAAATAGAACT
gi|343198619|ref|NR_043083.1|   CTAAAAGTTACCCCACCGAC    2   CTAAAGGTTACCCCACCGAC
gi|343201461|ref|NR_042187.1|   AACTGACAGTTTTAGAAACAGGACT   2   AATTGACAGTTTTAGAAATAGAACT

Here qcovs is in column 3.

[Karma]

Why don't you state the error that you are getting while running the command