interpreting RNAplfold output
Hi SEQanswers community,
I am using RNAplfold to get the probability of binding sites being single stranded, and got stuck trying to interpret the output _lunp files, and I can't find documentation on this format. As I understand, using the u flag with the length of the binding motif should give me information on accessibility of all kmers of the given length (probability of being single stranded). I used u 5 to get 5mer accessibility, which apparently generates 5 columns per position in the sequence. How do I interpret the numbers in the columns?
My guess is that the number of the column represents where this position is in the kmer, so each column will represent a different kmer containing this nucleotide. Which would mean that column 1 for position 1 represents the same kmer as column 2 for position 2. So, to get the accessibility of a certain kmer, I would guess that the values need to be averaged across the diagonals, so to say. However, I'm not sure if I'm interpreting these files right. Sometimes I get very different numbers between position 1, column 1 and position 2, column 2, and so on, and I would expect them to be more similar if my assumption was right. Anyone who can help me with how to interpret this?
