Question: Extension of reads
0
gravatar for madhu.9124
12 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 • 292 views
ADD COMMENTlink modified 12 months ago by shenwei3564.1k • written 12 months ago by madhu.912430

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

ADD REPLYlink written 12 months ago by ATpoint7.5k

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

ADD REPLYlink written 12 months ago by WouterDeCoster32k
0
gravatar for shenwei356
12 months ago by
shenwei3564.1k
China
shenwei3564.1k 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 12 months ago by shenwei3564.1k

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

ADD REPLYlink written 12 months ago by madhu.912430

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

ADD REPLYlink written 12 months ago by shenwei3564.1k
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