Quantifying RNA-seq data can be done either reference-free or using a reference genome (such as the human genome — GRCh38 being the latest version). There are multiple different alignment tools available, each one with its own specific parameters, options and algorithms. The most popular alignment tools are Cufflinks, HISAT2, STAR, Bowtie, BWA and TopHat. We use each of these tools in our analysis pipelines for different purposes.
Unguided transcriptome analysis
For some organisms a reference genome is not available, or the goal of the analysis is to discover new transcripts or isoforms. In such cases a de novo assembly of the sequence data is needed. Trinity is a software toolkit which allows reconstruction of complete transcripts from sequence data alone. We have extensive experience in unguided RNA-seq analyses, in both detection of novel isoforms and transcripts.
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