adult muscle
Raw reads were firstly processed through in-house perl scripts. In this step, clean reads were obtained by removing reads containing adapter, reads containing ploy-N and low quality reads from raw data. The rest reads were trimmed and cleaned by removing the sequences smaller than 15 nts or longer than 35 nts. Use Bowtie tools soft, The Clean Reads respectively with Silva database, GtRNAdb database, Rfam database and Repbase database sequence alignment, filter ribosomal RNA (rRNA), transfer RNA (tRNA), small nuclear RNA (snRNA), small nucleolar RNA (snoRNA) and other ncRNA and repeats. The remaining reads were used to detect known miRNA and novel miRNA predicted by comparing with Genome and known miRNAs from miRBase. Randfold tools soft was used for novel miRNA secondary structure prediction with a length of ~22 nts and free energy hybridization lower than 20 kcal/mol.
College of Animal Science and Technology, Henan University of Science and Technology