Question: Is There A Package To Map Primer Pair On Genome In R/Bioconductor?
gravatar for shangxiaoyun
5.2 years ago by
shangxiaoyun0 wrote:

Hi, everyone!

I have several primer pairs and want to map them onto genome, then calculate the coverage.

My plan now is as follows:

  1. using BSgenome to load the genome library;

  2. using function matchPattern in BSgenome to get the start and end information of the primer pairs;

  3. using function getseq to get sequences;

  4. alignment these sequences with genome sequence and calculate the coverage.

I'm wondering is there a packages which can map the primer pair on genome and get the sequences directly?

Thanks in advance!

bioconductor coverage primer • 2.0k views
ADD COMMENTlink modified 18 months ago by Biostar ♦♦ 20 • written 5.2 years ago by shangxiaoyun0

Hmmm. I've got a wrapper for invoking NCBI's e-pcr and importing a table of results...... What your after...?

ADD REPLYlink written 5.1 years ago by Malcolm.Cook790
gravatar for Dan
4.6 years ago by
Dan460 wrote:

Check this question: How to find a 28bp 'primer' sequence in a genome?

ADD COMMENTlink written 4.6 years ago by Dan460
gravatar for Ryan Thompson
4.6 years ago by
Ryan Thompson3.3k
TSRI, La Jolla, CA
Ryan Thompson3.3k wrote:

You could probably use Rsubread to map the primer pair as a paired-end dataset with only one pair in it. Make sure to set the appropriate options for multi-mapping and such.

ADD COMMENTlink written 4.6 years ago by Ryan Thompson3.3k
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