Dear all,
I am using standalone blast to blast a few hundred proteins against a custom database that I created (leido). I want a tabular output (displaying only the best hit) and the option -outfmt 6 is the best tested. I am using the following command to run it (pipping the output to gedit):
blastp -query subset.fasta -db leido -outfmt 6 -max_target_seqs 1 |gedit -
the output that I get (for this example, I am only submitting 3 proteins test wise (subset.fasta) follows and I know I am missing a few columns here - probably due to pasting issues in this text dialog, all columns appear on my gedit output though):
LmjF.36.6910 LdBPK_367240.1 98.88 537 6 0 1 537 1 537 0.0 1089
LmjF.36.6650 LdBPK_366960.1 96.75 553 18 0 1 553 1 553 0.0 1082
LmjF.36.5620 LdBPK_365870.1 96.77 1082 35 0 18 1099 19 1100
Is there a way to pass any flag to display the headers of the columns displayed in my output?
I tried already specifying the columns I want with (although I do not know whether or not this option should display the headers):
blastp -query subset.fasta -db leido -outfmt 6 "qseqid sseqid pident qlen length mismatch gapope evalue bitscore" -max_target_seqs 1 |gedit -
and I get the following error:
Error: Too many positional arguments (1), the offending value: qseqid sseqid pident qlen length mismatch apope evalue bitscore.
I can easily add the columns names in R, though I would like to explore all the standalone blast functionalities
Thanks
I'm actually interested in the -outfmt 6 format. But yes, I have to include the 6 inside the quotes. Blastp did not complain this time, though no header was displayed
Output format 7 (
outfmt 7
) goes with the header. Format 6 is the same, but without the header.Output format 6 = tabular while output format 7 = tabular with comment lines so the difference is not only the header.