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CSHL SEQTEC 2017 Transcriptome Assembly

In this workshop, we will be performing both genome-guided and genome-free transcript reconstruction.

For genome-guided reconstruction, we will leverage the Tuxedo2 protocol, leveraging HISAT2 tool for aligning RNA-Seq reads to a target genome, and StringTie for reconstructing transcript isoforms.

We will also leverage Trinity for genome-free transcript reconstruction, and compare our de novo assembled transcripts to the genome-guided reconstructions by aligning our Trinity transcripts to the target genome using GMAP and visualizing all the data using IGV.