RNA-seq Data Processing and Assembly

Raw data processing, base calling, and quality control were performed using RTA, OLB, and CASAVA (Illumina), according to the manufacturer’s pipeline. The output sequence quality was inspected using FastQC (http://www.bioinformatics.babraham.ac.uk/projects/fastqc/), and the reads were cleaned using cutadapt (version 1.8.1) [73 (link)] to trim low-quality ends (link)], yielding 49,239 contigs that clustered into 39,426 subcomponents (i.e., unigenes). The unigene sizes were 201 to 10,772 bp, with a mean length of 427 bp, N50 length of 1228 bp, and total combined length of 29,260,585 bp (Additional file 1: Table S1).

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Suzuki K., Suzuki T., Nakatsuka T., Dohra H., Yamagishi M., Matsuyama K, & Matsuura H. (2016). RNA-seq-based evaluation of bicolor tepal pigmentation in Asiatic hybrid lilies (Lilium spp.). BMC Genomics, 17, 611.

Publication 2016

CASAVA

Corresponding Organization :

Other organizations : Hokkaido University, Shizuoka University

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