Is There A Package To Map Primer Pair On Genome In R/Bioconductor?

Question

[shangxiaoyun]

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!

[Malcolm.Cook]

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

Answer 1

[Dan]

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

Answer 2

[Ryan Thompson]

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.