RNA_seq_pipeline (under development)

Alignment

DESeq2

Input files

salmon.output sampleFile

All differentially expressed genes

Count_matrix.xls.DESeq2.all.DE

PCA

Count_matrix.xls.DESeq2.normalized.rlog.pca.pdf

Hierarchical Clustering

Count_matrix.xls.DESeq2.normalized.rlog.pearson.pdf

rlog normalzied expression values

Count_matrix.xls.DESeq2.normalized.rlog.xls

size-factor normalized expression values

Count_matrix.xls.DESeq2.normalized.xls

run Rscript

Count_matrix.xls.DESeq2.r

Differentially expressed genes in different conditions

Count_matrix.xls.DESeq2.untrt.higherThan.trt.id.xls Count_matrix.xls.DESeq2.untrt.higherThan.trt.xls Count_matrix.xls.DESeq2.untrt.lowerThan.trt.id.xls Count_matrix.xls.DESeq2.untrt.lowerThan.trt.xls

visulizaiton for DE genes: volcano plot

Count_matrix.xls.DESeq2.untrt.vs.trt.results.xls Count_matrix.xls.DESeq2.untrt.vs.trt.results.xls.volcano.pdf