Flow chart: RNA-seq_statistics -> Cuffdiff, DESeq2, edgeR, ballgown

Quality check

Histogram of read counts by transcripts

MDS plot

Sample-to-sample Distances

Transcript

Differential transcript expression analysis by DESeq2 with scatter plot of read counts (counts per million)

	a
b	upregulated transcripts in a upregulated transcripts in b

Differential transcript expression analysis by edgeR with scatter plot of read counts (counts per million)

	a
b	upregulated transcripts in a upregulated transcripts in b

Differential transcript expression analysis by ballgown with scatter plot of read counts (counts per million)

	a
b	upregulated transcripts in a upregulated transcripts in b

Differential transcript expression analysis by Cuffdiff with scatter plot of read counts (counts per million)

	a
b	upregulated transcripts in a upregulated transcripts in b

Gene

Differential gene expression analysis by DESeq2 with scatter plot of read counts (counts per million)

	a
b	upregulated genes in a upregulated genes in b

Differential gene expression analysis by edgeR with scatter plot of read counts (counts per million)

	a
b	upregulated genes in a upregulated genes in b

Differential gene expression analysis by ballgown with scatter plot of read counts (counts per million)

	a
b	upregulated genes in a upregulated genes in b

Differential gene expression analysis by Cuffdiff with scatter plot of read counts (counts per million)

	a
b	upregulated genes in a upregulated genes in b