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Hi,
We focus on alternative splicing for one gene (with many exons).
We test several statistical methods (EdgeR, DESeq, DEXSeq) to identify DE exons, and we also calculate the PSI values with the IPSA package.
We know some exons as DE according to some biological experiments (in our lab + bibliography). We find some of them with the EdgeR or DESeq methods.
When we apply DEXseq method to our samples (4 samples x 2 conditions), we easily find a exon known as DE, but not a second exon (found as statisticaly DE with EdgeR and DESeq, and significant distinct PSI according to experimental conditions).
Why?
context :
Reads are single-end, 700nt length (454 sequencing), it's a targeted RNAseq (PCR baits in the 5' and 3'UTR of the gene).
The second exon not found is the penultimate exon..
Could anybody help us, please?
Thanks!
We focus on alternative splicing for one gene (with many exons).
We test several statistical methods (EdgeR, DESeq, DEXSeq) to identify DE exons, and we also calculate the PSI values with the IPSA package.
We know some exons as DE according to some biological experiments (in our lab + bibliography). We find some of them with the EdgeR or DESeq methods.
When we apply DEXseq method to our samples (4 samples x 2 conditions), we easily find a exon known as DE, but not a second exon (found as statisticaly DE with EdgeR and DESeq, and significant distinct PSI according to experimental conditions).
Why?
context :
Reads are single-end, 700nt length (454 sequencing), it's a targeted RNAseq (PCR baits in the 5' and 3'UTR of the gene).
The second exon not found is the penultimate exon..
Could anybody help us, please?
Thanks!