![]() ![]() ![]() Each cluster represents the full transcriptonal complexity for a given gene (or sets of genes that share sequences in common). ![]() Inchworm assembles the RNA-seq data into the unique sequences of transcripts, often generating full-length transcripts for a dominant isoform, but then reports just the unique portions of alternatively spliced transcripts.Ĭhrysalis clusters the Inchworm contigs into clusters and constructs complete de Bruijn graphs for each cluster. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-seq reads. Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Use the documentation links in the right-sidebar to navigate this documentation, and contact our Google group for technical support. Trinity -seqType fq -left reads_1.fq -right reads_2.fq -CPU 6 -max_memory 20Gįind assembled transcripts as: 'trinity_out_dir/Trinity.fasta'
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