filtering samples before normalization step
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11 weeks ago
rheab1230 ▴ 110

Hello, I want to do normalization for read count from the gtex portal. I was reading about gtex normalization for qtl analysis. The read count data is filtered by samples and gene. I am able to filter gene by CPM,read count. I am confused about sample filtering. The first filter is to remove replicated samples,outlier samples and sample with very low sequencing depth. Does anyone know how to filter based on these three criteria or any code for doing this. I checked my datasets it doesn't have replicated samples. Thank you.

TMM depth gtex normalization sequencing • 140 views
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I went through gtex portal qtl site but in that there is no filter for samples.

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