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!
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!