smncRNA analysis
Overview of the analysis
The small RNA-seq data was analysed with smrnaseq version 1.1.0 and excerpt version 4.3.2. The outputs of these pipelines were then analysed with the smncrna_analysis_template 3.2.5. The following treatment groups were compared for analysis:
- treatment1 vs. treatment2
- treatment1 vs. treatment3
The full analysis has been documented so others can take a “deep dive” into the analysis to check/reproduce the work.
Quality control reports
Both pipelines
excerpt
smrnaseq
RNA counts/expression
MDS/PCA plotting
RNA composition
Differential expression
limma/voom
- Differential expression (limma/voom)
- Differential expression volcano plots (limma/voom)
- Differential expression results (limma/voom)
deseq2
- Differential expression (deseq2)
- Differential expression MA plots (deseq2)
- Differential expression volcano plots (deseq2)
- Differential expression results (deseq2)
Both differential expression methods
Heatmaps
Presence/absence
Raw count data
Analysis workflow for reproducing this analysis
Outline where the project is located on which machine/server/cluster
Analysis located at /my_project/smncrna_analysis_template/ on ESR’s production network
Link your analysis documentation here
Extra
Provide link to your github repository with all your analyses
Find more in the github repository