Question: Ambiguous places in consensus
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gravatar for adrian18_07
7 weeks ago by
adrian18_0710
adrian18_0710 wrote:

I would like to make a consensus with the dumb_consensus function. Instead of the put "X" ambiguous place, I wanted to implement a selection of different possibilities. For example, if there is 'A' in one sequence, and 'T' in the other, it would nrmaly write 'X', but I want to reach 'W' instead of it. And as well If there would be 'C' and 'G' I want to get 'S' etc. Could someone help me to solve this problem?

Here is an example:

Seq1:

ATCGATC

Seq2:

AAGGAAG

Consensus:

AWSGAWS

Thanks for any answer.

ADD COMMENTlink written 7 weeks ago by adrian18_0710

To my knowledge you cannot do this with dumb_consensus specifically. You will need to write your own code to go column by column and decide what character to include, though this shouldn't be too difficult, its basically going to be a loop over the alignment/sequences, with a selection of if/else statements to decide what character to include.

ADD REPLYlink written 7 weeks ago by Joe18k

Thank you for the information.

ADD REPLYlink written 5 weeks ago by adrian18_0710
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