This could be a very silly question to ask, but pardon me for that.
I have Illumina paired end data and wanted to trim the reads for quality. Now I have already done fastqc and found that one R2 has poor quality after 225th bases (average read length is 250).
So should I trim both R1 and R2 to ensure paired read lengths are same i.e. 225? or it does not makes a difference if R1 and R2 reads have different lengths? I am going to assemble the reads using de novo approach so how will my decision affect the assembly. Please help.
Let me know if any further information is required from my end.