blastn command line

Question

[allifc]

Hi - I'm new to bioinformatics and trying to use the command line version of blastn. The web version of blastn has an option to show coding sequences near in or near any hits. I have not been able to find this option in any of the command line out-formats. Does anybody know if this is possible? Thank you!

[mark.ziemann]

I've had a look in the blastn help page and couldn't find any relevant options for nearby coding sequence, so there might not be a simple fix. The next best option could be to pass the tabular blastn results to a bedtools closest command.

[allifc]

Thank you for looking into it, bedtools is a great suggestion, I had not thought of that!