Assembly transcriptome

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...

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Bibliographic Details
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
Description
Summary: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.

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