This white paper explains some basic concepts related to alignment and mapping in Partek^® Genomics  Genomics Suite^™ (PGS) v6.6 under the RNA-seq workflow. The term “alignment” describes the process of finding the position of a sequencing read on the reference genome, while “mapping” refers to assigning already aligned reads to transcripts; it is also called quantification.

Number of Reads and Alignments 

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