_images/UnivLogo_Stack_2C_Dark.png

Differential gene expression analysis

Link for Bowtie mapped counts http://de.cyverse.org/dl/d/E9B4C299-D6CB-4656-A4F6-FF67240AEA49/170407_bowtie_counts.txt

Target file for bowtie mapped reads: http://de.cyverse.org/dl/d/BECB62C3-A369-4084-9BC9-2BFD9E6E9600/bowtie_target.txt

DESeq tutorial:

Tutorial link

Steps to perform DEseq analysis

  1. From Apps select “DEseq (Multifactorial Comparison)

    _images/DEseq_1.png

  1. Name your analysis and select a folder where your results need to be saved.

    _images/DEseq_2.png

  1. Select the correct target file and the count file.

    _images/DEseq_3.png

4. Give a name to the project. Reference biological condition should be “control” samples. Variable of interest is “group” (Column header of the third column of the target file).

_images/DEseq_4.png

  1. Set the significant threshold to 0.05 and launch the analysis.

    _images/DEseq_5.png

DE gene list

I have used the following R code to merge the DE genes list and the functions.

library(reshape2)
library(readr)

# Used the terminal command to grep the fasta headers and wrote it to a file called "ITAG3_10_cDN_names.txt"
#imported this file to Rstudio

# Removed the ">" sign
ITAG3_10_formated_names <- as.data.frame(sapply(ITAG3_10_cDN_names, gsub, pattern = ">", replacement = "" ))

#Seperate gene ids and description using space as delimiter
ITAG3_10_formated_names <- data.frame(colsplit(ITAG3_10_formated_names$X1, " ", c("Id", "Description")))

#imported up regulated genes to Rstudio and merge with the above file using gene ids.
heatvscontrol_up_func <- merge(heatvscontrol_up, ITAG3_10_formated_names,
                       by.x = "Id",
                       by.y = "Id")

#write output
write.table(x = heatvscontrol_up_func, file = "heatvscontrol_up_func.txt", quote = FALSE, sep = "\t", row.names = FALSE)


#imported down regulated genes to Rstudio and merge with the above file using gene ids
heatvscontrol_down_func <- merge(heatvscontrol_down, ITAG3_10_formated_names,
                       by.x = "Id",
                       by.y = "Id")
#write output
write.table(x = heatvscontrol_down_func, file = "heatvscontrol_down_func.txt", quote = FALSE, sep = "\t", row.names = FALSE)

Up-regulated gene list: http://de.cyverse.org/dl/d/E641698E-8688-4C20-B829-0B12BABC8ABB/heatvscontrol_up_func.txt

Down-regulated gene list: http://de.cyverse.org/dl/d/3C45B913-612F-4B97-8F44-8021470AE527/heatvscontrol_down_func.txt