davetang

#use chr22 as an example
#how many entries on the negative strand of chr22?
table(bam_df$rname == 'chr22' & bam_df$flag == 16)
# FALSE    TRUE 
#3875997   24413

#function for checking negative strand
check_neg <- function(x){
  if (intToBits(x)[5] == 1){
    return(T)

davetang

#install if necessary
install.packages('gtools')
#load library
library(gtools)
#urn with 3 balls
x <- c('red', 'blue', 'black')
#pick 2 balls from the urn with replacement
#get all permutations
permutations(n=3,r=2,v=x,repeats.allowed=T)
#      [,1]    [,2]   

davetang

#install if necessary
source("http://bioconductor.org/biocLite.R")
biocLite("Rsamtools")

#load library
library(Rsamtools)

#read in entire BAM file
bam <- scanBam("wgEncodeRikenCageHchCellPapAlnRep1.bam")

davetang

#!/bin/env perl

use strict;
use warnings;

print "My very first Gist on GitHub!\n";

exit(0);

__END__