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liulab-dfci / TRUST4

TCR and BCR assembly from RNA-seq data
MIT License
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How does the trimming work #292

Open ulyssebaruchel opened 1 month ago

ulyssebaruchel commented 1 month ago

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 commented 1 month ago

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.