Extension of reads

Question

[madhu.9124]

Hi,

I want to extend the read to the 3' or 5' end of the read. Kindly suggest some command.

[ATpoint]

Awk, and more elaborate: bedtools slop. In R: GenomicRanges package with the resize option.

[WouterDeCoster]

Please elaborate more on which data you have and what you aim to obtain. Your question doesn't contain sufficient information.

Answer 1

[shenwei356]

Well, a single read can't be extended.

• If you have a reference sequence: mapping reads to the reference and extend them.
• If reference is not available: assembling de novo, and extending reads.

[madhu.9124]

I mapped read to reference but any suggestions how to extend them?

[shenwei356]

retrieving mapping location and extending from reference by scripts or tools.

[boczniak767]

I have the same question. It is trivial to extend bed intervals, but what about extending mapped reads in bam file? I think samtools can't do that.