c parameter in MED pipeline

[Ed Smith]

Hi

I just wanted to check my interpretation that the 'c' parameter in the MED pipeline can be changed using the -d (maximum number of discriminants) input. Is that correct?

Thank you for developing such a powerful tool!

Cheers

Ed

[A. Murat Eren]

Hi Ed,

Do you mean the -c parameter in the oligotyping pipeline?

If yes, the answer is no :) -d, the maximum number of discriminants is the number of high entropy positions to be used by MED decomposition at every iteration. -c in the oligotyping pipeline indicates the nucleotide positions to be used to decompose a given set of reads in a single pass without any iteration.

I hope I am not missing your question completely.

Best,

--

A. Murat Eren (meren)
http://merenlab.org :: gpg

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