How are the reads assigned to genes in strand-specific RNAseq libraries?
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17 months ago
Sib ▴ 60

Hello Biostars,

I know that the benefit of strand-specific libraries is that we can assign the reads that fall into the overlap of the genes of the two DNA strands. I want to explain it by examples in forward-stranded and reverse-stranded libraries. So I have provided the following schema and I would be grateful if you could tell me if my explanation is correct:

enter image description here According to the schema:

  • In a forward-stranded library, reads mostly map on the same strand as the genes.

    So,

    Condition 1: If the direction of the read is forward, it can be concluded that the read should be assigned to the forward DNA strand (gene 1).

    Condition 2: If the direction of the read is reverse, the read should be assigned to the reverse DNA strand (gene 2).

  • In a reverse-stranded library, reads mostly map on the opposite strand as the genes.

    So,

    Condition 3: If the direction of the read is forward, it can be concluded that the read should be assigned to the reverse DNA strand (gene 2).

    Condition 4: If the direction of the read is reverse, it can be concluded that the read should be assigned to the forward DNA strand (gene 1).

I would appreciate it if you could tell me whether I am correct or not.

strand-specific strandness RNAseq • 439 views
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