index.md

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

• Sequencing read QC

excerpt

• Diagnostic plots

smrnaseq

• Mirtrace report
• MultiQC report

RNA counts/expression

• RNA expression plotting

MDS/PCA plotting

• MDS plots
• PCA plots

RNA composition

• RNA species composition - samples
• RNA species composition - treatments

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

• Differential expression - all results

Heatmaps

• Heatmaps

Presence/absence

• Presence/absence

Raw count data

• smrnaseq miRNA
• exceRpt miRNA
• exceRpt piRNA
• exceRpt tRNA
• exceRpt circularRNA
• exceRpt gencode

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

• setup.md
• running_excerpt_pipeline.md
• running_smrnaseq_pipeline.md
• master.Rmd

Extra

Provide link to your github repository with all your analyses

Find more in the github repository