pre-process RNA-seq?

[xy6699]

Hi,

Is it necessary to pre-process RNA-seq data before assembly?
FastQC can only check the quality but can't filter data. I saw some software for filtering like SeqTrim, TagDust.... But do we need to?

Cheers

[kopi-o]

If you are doing assembly, yes, it's important to get rid of bad-quality sequence. For mapping, it's generally speaking less important according to some benchmarks I've done, but it also depends a bit on which mapping software you are using.