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Old 05-31-2015, 01:48 AM   #1
zzy
Junior Member
 
Location: Beijing,China

Join Date: May 2013
Posts: 6
Default Trim to target in exome-seq

Dear all,
I am now analyzing some downloaded WES data to find SNPs and there certainly could have reads map to introns.
My questions are:
Should I remove these reads map to intons or just keep them? What difference does it make?
I plan to use USCS RefSeq Gene as annotation of exon boundaries, are there any notable difference between this annotation and exon array used to purify exome during experiment?

Thanks!
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