2.6 RNA-Seq Raw Data Clean and Alignment
Raw reads covering more than 2-N bases were first cast off. Then
adaptors and low-quality bases were removed from raw sequencing reads
using FASTX-Toolkit (Version 0.0.13). The short reads less than 16nt
were also discarded. Then, clean reads were aligned to the GRch38 genome
by tophat2 [28] allowing 4 mismatches. Uniquely mapped reads were
utilized for gene reads number counting and FPKM calculation (fragments
per kilobase of transcript per million fragments mapped) [29].