Assembly transcriptome

• Main Authors: Tong, Guang-Xiang, Xu, Wei, Zhang, Yong-Quan, Zhang, Qing-Yu, Yin, Jia-Sheng, Kuang, Youyi
• Format: Dataset
• Language: unknown
• Published: Dryad Digital Repository 2017
• Subjects: RNA-Seq; comparative transcript analysis; positive selection; microsatellite markers; Hucho taimen
• Online Access: https://dx.doi.org/10.5061/dryad.9gd3n/6; http://datadryad.org/resource/doi:10.5061/dryad.9gd3n/6

The transcriptome sequences were assembled using the Trinity package. Before assembly, low-quality reads were filtered from the raw reads using Trimmomatic with the parameters LEADING:20 TRAILING:20 SLIDINGWINDOW:4:20 MINLEN:50. The clean reads from the two pooled libraries were merged and in silico normalized using the Trinity package with default parameters to reduce the running time and memory consumption. A parameter kmer size of 25 and a depth of at least two kmer were used for assembly with the Trinity package. The contigs resulting from Trinity were further fed to the TGI clustering Tool (version 2.1) to process alternative splicing and redundant sequences.The raw RNA-Seq reads and assembled transcripts were deposited in the European Nucleotide Archive under the project ID PRJEB19675 and accession numbers HAGJ01000001 to HAGJ01190473 for the assembled transcripts.