I don't know if you use RetroSeq to detect transposable element but I have an issue with it :
* FATAL ERROR *: Unrecognised symbol 'x' (ascii:120) file:[17846.allrefs.fasta] seq:[Endogenous_retrovirus] pos: exiting ...
I checked the file (which is the file with the TE sequences) and saw that in fact there are some x, k, etc. in it. How can I deal with it?
Thank you for your help! Lou