Question: Extension of reads
0
gravatar for madhu.9124
9 months ago by
madhu.912430
madhu.912430 wrote:

Hi,

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

sequence • 262 views
ADD COMMENTlink modified 9 months ago by shenwei3563.8k • written 9 months ago by madhu.912430

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

ADD REPLYlink written 9 months ago by ATpoint4.4k

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

ADD REPLYlink written 9 months ago by WouterDeCoster29k
0
gravatar for shenwei356
9 months ago by
shenwei3563.8k
China
shenwei3563.8k wrote:

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.
ADD COMMENTlink written 9 months ago by shenwei3563.8k

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

ADD REPLYlink written 9 months ago by madhu.912430

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

ADD REPLYlink written 9 months ago by shenwei3563.8k
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