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Fig. 7 | Plant Methods

Fig. 7

From: A phenol/chloroform-free method to extract nucleic acids from recalcitrant, woody tropical species for gene expression and sequencing

Fig. 7

Sequence quality of RNA extracted using the CTAB/SDS RNA extraction protocol. RNA was assessed by producing high-throughput RNA sequencing (RNA-seq) libraries of the avocado, macadamia and mango samples shown in Figs. 1, 2, 3, 4 and 5. The RNA-Seq libraries were pair-end sequenced (150 bp) on the Illumina 2500 Hi-Seq Platform. Sequencing quality assessment using FastQC version 0.10.1 [9] is represented in graphs describing quality across all bases from every sequence read at each position (a Avocado; b Mango; c Macadamia, respectively). Sequence quality is based on phred scores, an exponential scale where, for example, 20 = one incorrect sequence base-call in 100, and 30 = one incorrect base-call in 1000. The y-axis shows the quality scores, and the higher the score, the greater confidence in the base-calls at that position. The background of the graph divides the y-axis into very good quality calls (green), reasonable quality (orange), and poor quality (red). The graphs are representative of the forward reads (for reverse reads, see Additional file 2: Fig. S2)

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