Flow chart: RNA-seq -> HISAT2, StringTie, Cuffdiff

graph LR; A((FASTQ))-->B{PRINSEQ 0.20.4}; B-->C{HISAT2 2.1.0} C-->D{StringTie 1.3.4} D-->E(reference guided assembled transcripts) E-->F{StringTie merge 1.3.4} A2((FASTQ))-->B2{PRINSEQ 0.20.4}; B2-->C2{HISAT2 2.1.0} C2-->D2{StringTie 1.3.4} D2-->E2(reference guided assembled transcripts) E2-->F F-->G(merged transcripts) A-->H{Cuffquant 2.2.1} A2-->H G-->H A-->I{ballgown count} A2-->I G-->I H-->J{Cuffdiff 2.2.1} I-->K{DESeq2 1.22.2} G-->L{Trinotate v3.1.1} I-->M(annotated gene expression table) L-->M M-->N(0_result.html) J-->N K-->N O[sample_information.txt]-.->J O-.->K P[reference GTF]-.->F I-->Q{ballgown 2.14.1} O-.->Q Q-->N

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

GO

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

	a
b	upregulated gos in a upregulated gos in b

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

	a
b	upregulated gos in a upregulated gos in b

Data download