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Old 11-23-2016, 11:41 PM   #1
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Location: SE Asia

Join Date: Oct 2016
Posts: 4
Default "bioinformatically pooling" replicates for SNP discovery from Pooled RNA-seq

Dear all,

What I have:
3 populations duplicate, 25M 100-PE reads each. That will be 6 libraries (using sample > 40 per lib) all in all.

Objective: discover SNP and use it for SNP genotyping and pop gen studies


Should I just combine Pop1_replicate1 and Pop1_replicate2 libraries (e.g., concatenate the two read1's and two read2's to get finalread1 and 2) before doing alignment, sorting, and SNP discovery? Any thoughts?

jfo is offline   Reply With Quote

pooled sequencing, rna-seq analysis, snp calling

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