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17 minutes ago by

University Park, USA

The summary is that it depends on the sequencing instrument and on the protocol. Most common protocols (Illumina Trueseq) do end up producing reads that match the antisense of how to feature is annotated in say the genomic build.

For example, as you noted, all single end reads that originate from a transcript that happens to be annotated on the forward strand will match on the reverse strand (reverse complemented).

But this property is solely determined by the sequencing protocol and is not an inherent property of RNA-Seq data in general.

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Istvan Albert ♦♦ 85k



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