RNA-seq Analysis Workshop Course Materials

Listed below are the course materials for the R workshop. To download the following files, right click on the link and select "Save Target As..."

Course Notes

• Complete course notes: Intro2RNAseq.pdf
• Slides (day1):Slides_Nov2019_Day1.pdf [14M]
• Slides (day2):Slides_Nov2019_Day2.pdf [13M]
• Slides (day3):Slides_Nov2019_Day3.pdf [4.6M]
• Slides (day4):Slides_Nov2019_Day4.pdf [2.8M]

Additional scripts

R markdown files of all commands used are available here:

• Friederike's GitHub page

Sample alignment files

• WT_1_Aligned.sortedByCoord.out.bam [271M]; WT_1_Aligned.sortedByCoord.out.bam.bai [45K]
• WT_2_Aligned.sortedByCoord.out.bam [375M]; WT_2_Aligned.sortedByCoord.out.bam.bai [48K]
• SNF2_1_Aligned.sortedByCoord.out.bam [491M]; SNF2_1_Aligned.sortedByCoord.out.bam.bai [53K]
• SNF2_2_Aligned.sortedByCoord.out.bam [406M]; SNF2_2_Aligned.sortedByCoord.out.bam.bai [46K]

Sample read count table

• featCounts_genes.txt [499K]

Sample QoRTs output

• QC.multiPlot.pdf [58K]

Sample multiQC output

• multiqc_report.html
• multiqc_report_postAlign.html

Manuals

• FastQC tutorial (MSU Core Facility) [815K]
• STARmanual.pdf [246K]
• DESeq2
• edgeR [1.5M]
• limma [1.2M]

R data

• Rclass.RData [638K]

GO analysis data

• genesGotest.txt

For further information please contact Friederike Dündar, Paul Zumbo or Luce Skrabanek

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