Question: Convert blast tabular output to bed format
1
gravatar for Denis
17 months ago by
Denis120
Denis120 wrote:

I need to convert blast output in tabular format (format 6) to bed format. I'm interested only in qstart and qend coordinates (the 7th & 8th columns respectively). As far i know bed format is 0-based, but blast probably uses 1-based coordinates. Am i right?

So to do so with AWK i need to execute the code below:

cat balst_tabular_output.txt | awk '{print($2"\t"$7-1"\t"$8)}' > blast_otput.bed
genome • 992 views
ADD COMMENTlink written 17 months ago by Denis120

I've manually checked blast output and corresponding query sequences. So, blast definitely uses 1-based coordinates.

ADD REPLYlink written 16 months ago by Denis120
3
gravatar for cschu181
17 months ago by
cschu1811.8k
cschu1811.8k wrote:

Yes, BLAST is 1-based and your conversion should be right (keeping qend 1-based makes it compatible with the open interval style that bed uses.)

ADD COMMENTlink written 17 months ago by cschu1811.8k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1733 users visited in the last hour