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-   -   RNASeq: Multiple identical uniquely mapped reads (http://seqanswers.com/forums/showthread.php?t=43690)

Fernas 05-28-2014 07:15 AM

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.

Chipper 05-28-2014 07:54 AM

Quote:

Originally Posted by Fernas (Post 141442)
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.

Fernas 05-28-2014 08:03 AM

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


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