I wanted to know whether I need to remove the primer sequences from raw data before giving it to ITSxpress. Can hmm matching and trimming handle those sequences?
Because when I am running the ITSxpress with cutadapt trimmed data, I am losing too many reads after trimming in ITSxpress.
Do i need to remove the primer sequences (cutadapt) before using ItSxpress for Fungal ITS data or the hmm matching and trimming can handle that for me?
It has been a long while since I've used ITSxpress, but my recollection is that it is better leave the primers in the sequences for ITSxpress. Doing so will make it easier for the model to find and extract the ITS sequences. But things may have changed since I've used this...
Perhaps others with more recent experience can comment on this?