Can I do paired-end sequencing with mRNA-Seq libraries?

MRNA-Seq libraries are built with paired-end adapters and amplification primers. They can be run on paired-end flow cells, and two paired runs of sequence data will be generated. However, these paired sequences can span unknown splicing junctions, which complicates alignment to a reference transcriptome.

For this reason, Illumina does not support this application. However, users with bioinformatics experience can create their own alignment methods to handle these paired reads. More.

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