Table 2.
Correlation of trimmed and untrimmed RNA-seq data with the TaqMan RT-PCR data
| 100 bp PE | 50 bp SE | |||
|---|---|---|---|---|
| Method | UHRR | HBRR | UHRR | HBRR |
| No trimming + Subread | 0.851 | 0.870 | 0.848 | 0.870 |
| Trimmomatic–adapters and SW + Subread | 0.850 | 0.870 | 0.848 | 0.869 |
| Trimmomatic–adapters and MI + Subread | 0.850 | 0.871 | 0.849 | 0.869 |
| TrimGalore + Subread | 0.850 | 0.870 | 0.849 | 0.869 |
Shown are the coefficients of Pearson correlation between log2 expression values of 949 genes measured by the TaqMan RT-PCR technique and their RNA-seq expression levels generated from using each method (log2-RPKM). ‘100 bp PE’ in the table denotes the 100 bp paired-end SEQC dataset. First reads (R1 reads) in this dataset were extracted and truncated to 50 bp long to generate the 50bp single-end dataset used here (‘50 bp SE’).