Question: Extension of reads
0
gravatar for madhu.9124
4 weeks ago by
madhu.912410
madhu.912410 wrote:

Hi,

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

sequence • 130 views
ADD COMMENTlink modified 4 weeks ago by shenwei3563.4k • written 4 weeks ago by madhu.912410

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

ADD REPLYlink written 4 weeks ago by ATPoint1.6k

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

ADD REPLYlink written 4 weeks ago by WouterDeCoster22k
0
gravatar for shenwei356
4 weeks ago by
shenwei3563.4k
China
shenwei3563.4k 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 4 weeks ago by shenwei3563.4k

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

ADD REPLYlink written 29 days ago by madhu.912410

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

ADD REPLYlink written 29 days ago by shenwei3563.4k
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