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  • RNASeq: Multiple identical uniquely mapped reads

    Hi all,

    My question is about processing RNASeq data in order to extract the normal gene expression count matrix:

    if two reads are mapped uniquely to the same genome position and both of them have identical alignment region. Shall we count them as 2 reads or simply 1.

    If you say that we count them as 2 reads, then my question: why in Chipseq processing, we count these 2 reads as only 1 to remove the PCR bias problem which may cause such duplicates.

  • #2
    Originally posted by Fernas View Post
    Hi all,

    My question is about processing RNASeq data in order to extract the normal gene expression count matrix:

    if two reads are mapped uniquely to the same genome position and both of them have identical alignment region. Shall we count them as 2 reads or simply 1.

    If you say that we count them as 2 reads, then my question: why in Chipseq processing, we count these 2 reads as only 1 to remove the PCR bias problem which may cause such duplicates.
    De-duplication would not let you analyze highly expressed transcripts which will need to have many identical reads. If you think your RNA-seq sample has a high PCR duplication rate it is better to downsample it.

    Comment


    • #3
      Thanks @chipper.
      But I am still wondering why in Chipseq processing steps, we remove duplicates, however, in RNASeq we keep them.

      Comment

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