Additional file 1: Table S1. of QuickMIRSeq: a pipeline for quick and accurate quantification of both known miRNAs and isomiRs by jointly processing multiple samples from microRNA sequencing

Human mature miRNAs in miRBase Release 21 with identical sequences. Table S2. Human hairpins in miRBase Release 21 with identical sequences. Table S3. Pairs of miRNAs that are reverse complementary to each other in human miRBase Release 21. Table S4. Top 10 miRNAs with large differences in miRNA quantification between stranded and non-stranded mapping modes. Table S5. Distribution of 5′ and 3′ end offsets of unique miRNA reads in GSE64977. Figure S1. Top panel: All of the miRNAs in the alignment have the same mature sequence (highlighted in gray), but originate from different genes as evidenced by the differences in the pre-miRNA sequences. Bottom panel: miRNA genes found in a cluster on human chromosome 19. Figure S2. Protocol of isomiR quantification. Figure S3. Scatter plots of miRNA quantification results by miRge for samples SRR1759212 SRR1759213, SRR1759214 and SRR1759215. The same dataset were analyzed with and without incorporation of the strand information, respectively. Figure S4. Breakdown of mapped miRNA reads into perfect and mismatch categories. Figure S5. Comprehensive annotation of miRNA-seq reads. The summary plot provides an overview of the distribution of annotated reads in all five annotated RNA categories for each sample. Figure S6. Summary report for adapter trimming. Figure S7. Read length distributions for samples SRR1759212, SRR1759213, SRR1759214, and SRR1759215 in the GSE64977 miRNA-seq dataset. Figure S8. Variations at 5′ and 3′ ends of miRNA reads. Figure S9. The comparison of QuickMIRSeq with miRge. (PDF 1088 kb)