Hi,

I am trying to use SeqLogo to analyze small RNA-seq data.

However, when I am generating a Position Weight Matrix (PWM) from my data, I can only generate a PWM with probability values that do not add up to 1.

Unfortunately this is the requirement to run seqLogo.

So, my question is: How can I generate a PWM from my fasta input file with colums adding up to 1 ??

Thanks a lot for your help,

Claus.

Hi clausdkuhn, 

Please see ?Biostrings::matchPWM for more details. 

Regards,

Marcel