Pinned

1. intersect_count.sh intersect_count.sh

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   ##takes output from bedtools intersect output tab delimted file containing all instances at which two annotations intersect 

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   ##bedtools intersect input of alignment.bed file and gff/gtf3 annotation 

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   ##script output count table of unique gene ID and number of intersect counts (collapsed under one gene id)

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   function count_intersect() {

2. graph_genescf_output.R graph_genescf_output.R

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   #requires tab delimited output file after running genescf

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   #re-generates default scatterplot output from genescf with improved readability 

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   #requires two arguments from r console: imported raw genescf output table and name of sample group

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   graph_genescf <- function(table, name){