hi all,
i have a question about my problem in rna-seq with my sample.
i have 25 different sample from 25 human and i sequence them by rna-seq to find variant calling by Tophat,mpileup and VarScan.
My result is also good when some sample's SNP are found on dbSNP, but i have a problem when some sample have SNP in intron region(many reads is mapping into this SNP, it 's not a noise), how can i explain this problem ? is it noise in sequencing or is there some mechanism intron region can come with mature mRNA in human ?
Thank you all.
i have a question about my problem in rna-seq with my sample.
i have 25 different sample from 25 human and i sequence them by rna-seq to find variant calling by Tophat,mpileup and VarScan.
My result is also good when some sample's SNP are found on dbSNP, but i have a problem when some sample have SNP in intron region(many reads is mapping into this SNP, it 's not a noise), how can i explain this problem ? is it noise in sequencing or is there some mechanism intron region can come with mature mRNA in human ?
Thank you all.
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