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.
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.
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