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Old 06-15-2014, 10:10 PM   #1
shangzhong0619
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Location: La Jolla

Join Date: Nov 2013
Posts: 17
Default Does Strand-specific RNA-seq mean reads from one genome strand?

Hi all,
I got a little bit confused about the strand specific RNA-seq. I saw the dUTP protocol to generate strand specific RNA seq, it seems that it amplifies the sequence which is complement to mRNA. But since some mRNA may have same sequence with the sense genome strand, some may have same sequence with antisense genome strand. In this case, the reads from one fastq file may map to both strand of reference genome, right? In my understanding, reads in one fastq file should from the same strand.

Or the strand specific only refers to mRNA sequence, doesn't care about the genome strand? In other words, mRNA has the same sequence with forward strand, but different mRNA's forward strand may refer to different genome strand. So in one fastq file, all the reads are in one direction with respect to mRNA, and they can map to two strands of genome DNA. Is this right?

Any comments would be appreciated. Thanks
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