Question about fastp trimming

[KevinMer]

Hello,

thanks to share this pipeline.

I was wondering why fastp trimming is only used with FusionCatcher but not with Arriba and Star-fusion ?
Did you perform any benchmark leading to this choice ? Or do you have some references ?

Thanks a lot for your answer,

Best regards,

Kevin

[rannick]

Hello,
fastp trimming is performed twice (optionally): Once for all reads when quality trimming and adapter trimming is done and another time without those trimming just to trim reads larger than 100 bp to feed into FusionCatcher as anything more will lead to an overwhelming number of false positives.