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eclarke / swga

Select primer sets for selective whole genome amplification (SWGA)
GNU General Public License v3.0
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Masking repetitive regions #35

Open sesh-sas opened 8 years ago

sesh-sas commented 8 years ago

Short sequences repeated many times (i.e. telomeres) can result in the generation of poor sets with primers that bind many times within a very short distance. Masking these regions would probably improve set finding.

eclarke commented 8 years ago

Do we want to incorporate this into the program itself or recommend that people run a third-party program like dust beforehand?

sesh-sas commented 8 years ago

If we could find a good program that is easy to install, then running the third party program would be easier, better.

On Apr 24, 2016, at 1:59 PM, Erik Clarke notifications@github.com wrote:

Do we want to incorporate this into the program itself or recommend that people run a third-party program like dust beforehand?

— You are receiving this because you authored the thread. Reply to this email directly or view it on GitHub https://github.com/eclarke/swga/issues/35#issuecomment-214010057

eclarke commented 8 years ago

We can use the bioconda repo for installing the BLAST+ suite and then have people use dustmaker. In fact, we could probably switch to conda/bioconda as the preferred install/workspace environment.

I need to write test cases to make sure dsk works with masked regions. Have you inputted sequences with lots of Ns?