Hi, we obtained pared-end RNA-Seq data from Illumina.Unfortunately, the reads are not of the same length. The length of first reads is 100bp, while the second reads is 97bp. I have two questions about the read length.
(1). I wonder whether it is necessary to do read trimming so that both reads are of the same length. I know that most mapping tools are not care the disparate read lengths between a pair.
(2). In addition, I wonder whether it is necessary to use trimming tools to cut a read if below a threshold quality. I think most mapping tools can deal with base call qualities, so it is no need to trim reads. Is it correct? Thanks.