How does the trimming work

[ulyssebaruchel]

Hi, it seems there is low quality trimming done by default. May I ask how it works, please? I could not find the information anywhere. Is there a way to turn it off, also?
Thank you very much.

[mourisl]

There are other trimmings in TRUST4 that cannot be turned off now. For example, when there is read-through event in paired-end data, the putative adapter sequence will be trimmed. Another scenario is when the read is found to overlap with V and part of it is before the 5' of V gene, then those over-hang region will be trimmed.