With QuantSeq REV and the Custom Sequencing Primer, it is possible to exactly pinpoint the 3' end during Read 1. The reads generated during Read 1 reflect the cDNA sequence, beginning at the start of the poly(A) tail and are therefore reading back into the transcript sequence. Therefore Read 1 reads are in a strand orientation opposite to the genomic referencethe mRNA sequence. The Read 2 read directly reflects the mRNA sequence and reads towards the poly(A) tail.
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