Trimming reads generated by the template switching RT

[Ahram-Ahn]

Hi,

I have a technical question regarding the trimming step. In the case that template switching reverse transcriptase is used, is it necessary to trim additional 3nt from one end to remove the added nucleotides? Should we do it only for the 5'end and use -u 3 command?

Thanks,

[marcelm]

Without more context, I don’t know how to run it in this particular case. I may be able to help if you post an example read and the command that you intend to run.