Green ash RNASeq analysis scripts

The software contained here was used to perform analyses on green ash transcriptome data collected by the Staton lab.

• degs.R
• hclust_dendro.R
• hm_bingo.R

Version

02.22.2016

degs.R

degs.R (differentially expressed genes) is an Rscript used to calculate and construct some of the figures/tables in the manuscript "De novo assembly of the green ash transcriptome and identification of genes responding to abiotic and biotic stress" Lane et. al. 2015

degs.R assumes a directory in home called "degs" exists degs.R also assumes a sub-directory in home called counts-sorted exists and contains HTSeq output from green ash libraries. See counts-sorted.zip.

degs.R will create two directories for outputs: output and images

• counts-sorted

counts-sorted

This directory contains the counted read data from HTSeq across the green ash libraries. This data is needed for input into the degs.R script.

hclust_dendro.R

hclust_dendro.R is an Rscript used to use rpkm normalized values and generate clustered output in "De novo assembly of the green ash transcriptome and identification of genes responding to abiotic and biotic stress" Lane et. al. 2015

hclust_dendro.R assumes a directory in home called "hclust_dendro" exists hclust_dendro.R also assumes a sub-directory in home called rpkm containing "all_final_cut55.tsv" a file of rpkm normalized values accross 55 green ash libraries. This file can be produced using the code in the rpkm directory

hclust_dendro.R will create a single output Tiff "hclust_dendro.tiff"

• rpkm

rpkm

This directory contains the scripts for calculating RPKMs which are used as input for the hclust_dendro.R. A compressed version of the input file "all_final_cut55.tsv.gz" is also included.

hm_bingo.R

hm_bingo.R (heatmap bingo) is an Rscript used to read in BiNGO GO enrichment results and generate a heatmap used in "De novo assembly of the green ash transcriptome and identification of genes responding to abiotic and biotic stress" Lane et. al. 2015

hm_bingo.R assumes a directory in home called "hm_bingo" exists hm_bingo.R also assumes a sub-directory in home called bgo exists and contains headless output from BiNGO.

Headless output from BiNGO can be generated by saving output from BiNGO and parsing out all lines that begin with "GO-ID". For example using grep:

$ grep "^GO-ID" ColdOUTPUT.bgo > headless_ColdOUTPUT.bgo

hm_bingo.R will create a three output Tiff files "Figure5_all.tiff," "Figure5A_up.tiff," and "Figure5B_down.tiff"

• bgo
• Cold_down_old
• Cold_up_old
• goSlim_greenAsh.GAF

bgo

This directory contains the GO Term enrichments from running Bingo. These serve as the inputs for hm_bingo.R.

Cold_down_old

An old version of the Cold_down output from Bingo.

Cold_up_old

An old version of the Cold_up output from Bingo.

goSlim_greenAsh.GAF

This is another necessary input for running Bingo.