brianjmpark

#requires tab delimited output file after running genescf
#re-generates default scatterplot output from genescf with improved readability 
#requires two arguments from r console: imported raw genescf output table and name of sample group

graph_genescf <- function(table, name){
  require(ggplot2)
  require(plyr)
  table <- table[,c(2,3,4,5,6)] 
  table <- arrange(table, P.value)
  table <- table[1:20,]

brianjmpark

##takes output from bedtools intersect output tab delimted file containing all instances at which two annotations intersect 
##bedtools intersect input of alignment.bed file and gff/gtf3 annotation 
##script output count table of unique gene ID and number of intersect counts (collapsed under one gene id)

function count_intersect() {
	echo "using file name $1.tsv"
	cut -f15 $1_intersect_final.tsv |
  tail -n +2 |
  awk -F '[;]' '{print $2}' |
  awk -F '["]' '{print $2}' |