I want to extend the read to the 3' or 5' end of the read. Kindly suggest some command.
Awk, and more elaborate: bedtools slop. In R: GenomicRanges package with the resize option.
Please elaborate more on which data you have and what you aim to obtain. Your question doesn't contain sufficient information.
Well, a single read can't be extended.
I mapped read to reference but any suggestions how to extend them?
retrieving mapping location and extending from reference by scripts or tools.