Hi everyone:
I'm not quite familiar with RNA-seq alignment. It seems that part of the RNA-seq reads (splice site) can be mapped to reference genome by alignment tool Tophat or STAR. In this case, do we need to remove the adapters for sequencing reads with tools like cutadapt? For small RNA-seq, since the sequencing reads length is increasing, there is high possibility that the reads will contain adapter sequences.
Thanks, which trim tool would you suggest?
There are two popular ones cutadapt and fastx clipper
I would go for cutadapt,
Thanks, cutadapt is a good tool.