GLAM2 motif logos: U instead of T?

[Kate Nie]

Hi,

I'm trying to use GLAM2 for RNA motif prediction. It look like the default option for nucleotides (option 'n') only generates DNA motif logos. Is there a way to get U instead of T in the output logos?

Best,

Kate

[CharlesEGrant]

The public web application for GLAM2 will always translate 'U' to 'T' as it reads the sequences. If you are using the command line version of GLAM2 you may be able to specify a custom alphabet using the RNA symbols. For more information on using custom alphabets with GLAM2 see the GLAM2 tutorial.