Entering edit mode
4.3 years ago
adrian18_07
▴
10
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.
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 ofif/else
statements to decide what character to include.Thank you for the information.