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In Illumina Stranded RNA-Seq (using the dUTP method), do the final reads in the fastq files correspond to the initial molecule (that was transcribed), or to the reverse complement of the molecule?
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It will be different for read 1 and read 2. For the dUTP stranded protocol read 1 is the reverse complement of the mRNA, read 2 matches the sequence and direction of the mRNA. Further, read 2 should be positioned to the left (5') of read 1, when considered in transcript coordinate space.Originally posted by carmeyeii View PostIn Illumina Stranded RNA-Seq (using the dUTP method), do the final reads in the fastq files correspond to the initial molecule (that was transcribed), or to the reverse complement of the molecule?
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Thanks kmcarr,
So the strand with the same sequence and direction of the mRNA is the one retained for the first phase of paired-end sequencing, covalently linked through the P7 adapter?
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my brain is now at rest.
thank you.Comment
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