decodebiology

#Rscript normalize_featurecounts.R counts_table.txt tpm ;
#Rscript normalize_featurecounts.R counts_table.txt rpkm ;

#Sample table###

#GeneID<TAB>sample1<TAB>sample2<TAB>sample3<TAB>Length
#Gene1<TAB>10<TAB>4<TAB>5<TAB>1500
#Gene2<TAB>20<TAB>43<TAB>60<TAB>4300

decodebiology

#!/bin/bash
# ./CheckPhredScale.sh <FASTQ_FILE> <NUMBER OF LINES TO CHECK>
echo "Shell:";

zcat $1 | head -n $2 | awk '{if(NR%4==0) printf("%s",$0);}' |  od -A n -t u1 | awk 'BEGIN{min=100;max=0;}{for(i=1;i<=NF;i++) {if($i>max) max=$i; if($i<min) min=$i;}}END{if(max<=74 && min<59) print "Phred+33"; else if(max>73 && min>=64) print "Phred+64"; else if(min>=59 && min<64 && max>73) print "Solexa+64"; else print "Unknown score encoding";}';
echo "";
echo "python:";

zcat $1 | awk 'NR % 4 == 0' | head -n $2 | python ./guess-encoding.py

decodebiology

#!/usr/bin/perl 
$/=undef;
## Run script: perl CpG_feature_extraction.pl CpG_islands.bed shores/shelves (This gives warnings for 'rm' command, just ignore it)
# Reference for definition of shores and shelves from:
# http://www.mdpi.com/2073-4425/5/2/347/htm
# http://www.mdpi.com/genes/genes-05-00347/article_deploy/html/images/genes-05-00347-g001-1024.png
extend_coordinates($ARGV[0] ,$ARGV[1]);
sub extend_coordinates
{
	$type=$ARGV[1];

decodebiology

#USAGE: CI_normal(matrix[,c(x:y)],97.5) - multiple column from a normal distribution
#USAGE: CI_tdist(matrix[,c(x:y)],97.5) - multiple column from a t distribution
#USAGE: CI_normal(matrix[,x],97.5) - single column from a normal distribution
#USAGE: CI_tdist(matrix[,x],97.5) - single column from a t distribution
#Created and updated by Santhilal Subhash on 2016/06/07 
CI_normal <- function(li,stat)
{
	cat(paste0("CI","\t","column","\t","Lower.limit","\t","Upper.limit","\n"))
	if(length(colnames(li))>1)
	{

decodebiology

m.row.sum<- cbind(m1, rowSums(m1))
o1<- rev(order(m.row.sum[,602]))

m.row.sum<- m.row.sum[o1,]

bk = unique(c(seq(-0.1,3, length=100),seq(3,10.35,length=100)))

hmcols<- colorRampPalette(c("white","red"))(length(bk)-1)

pheatmap( m.row.sum[,1:601], cluster_rows = F, cluster_cols = F, col= hmcols, breaks = bk, legend=FALSE, show_rownames=FALSE, show_colnames=FALSE)

decodebiology

#The X axis is -3 kb to 3 kb around TSS.

#It turns out that the heatmap.2 function use default hclust ( Hierachical Clustering) to cluster the #matrix.
#alternatively, we can use K-means clustering to cluster the data and to see what's the pattern look like.

km<- kmeans(m1,2)   # determine how many cluster you want, I specify 2 here

m1.kmeans<- cbind(m1, km$cluster)   # combine the cluster with the matrix

dim(m1.kmeans)

decodebiology

# This R script is to generate the TF or histone modification heatmap
# at certain genomic features (TSS, enhancers) from the ChIP-seq data
# the input matrix is got from Homer software. alternative to R, use cluster3 to cluster, and visualize by # java Treeviewer
# generate the matrix by Homer: annotatePeaks.pl peak_file.txt hg19 -size 6000 -hist 10  -ghist -d TF1/ # > outputfile_matrix.txt
# see several posts for heatmap:
# http://davetang.org/muse/2010/12/06/making-a-heatmap-with-r/
# http://www.r-bloggers.com/r-using-rcolorbrewer-to-colour-your-figures-in-r/
# 08/20/13 by Tommy Tang

# it is such a simple script but took me several days to get it work...I mean the desired

decodebiology

ENST00000423562	chr1	14363	29370	-	ENSG00000227232	WASH7P	pseudogene
ENST00000438504	chr1	14363	29370	-	ENSG00000227232	WASH7P	pseudogene
ENST00000450305	chr1	12010	13670	+	ENSG00000223972	DDX11L1	pseudogene
ENST00000456328	chr1	11869	14409	+	ENSG00000223972	DDX11L1	pseudogene
ENST00000469289	chr1	30267	31109	+	ENSG00000243485	MIR1302-11	lincRNA
ENST00000473358	chr1	29554	31097	+	ENSG00000243485	MIR1302-11	lincRNA
ENST00000488147	chr1	14404	29570	-	ENSG00000227232	WASH7P	pseudogene
ENST00000515242	chr1	11872	14412	+	ENSG00000223972	DDX11L1	pseudogene
ENST00000518655	chr1	11874	14409	+	ENSG00000223972	DDX11L1	pseudogene
ENST00000538476	chr1	14411	29806	-	ENSG00000227232	WASH7P	pseudogene

decodebiology

ENSG00000223972	chr1	11869	14412	+	DDX11L1	pseudogene
ENSG00000227232	chr1	14363	29806	-	WASH7P	pseudogene
ENSG00000243485	chr1	29554	31109	+	MIR1302-11	lincRNA

decodebiology

chr1	processed_transcript	exon	11869	12227	.	+	.	gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "1"; gene_name "DDX11L1"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; exon_id "ENSE00002234944";
chr1	processed_transcript	exon	12613	12721	.	+	.	gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "2"; gene_name "DDX11L1"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; exon_id "ENSE00003582793";
chr1	processed_transcript	exon	13221	14409	.	+	.	gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; exon_number "3"; gene_name "DDX11L1"; gene_biotype "pseudogene"; transcript_name "DDX11L1-002"; exon_id "ENSE00002312635";
chr1	transcribed_unprocessed_pseudogene	exon	11872	12227	.	+	.	gene_id "ENSG00000223972"; transcript_id "ENST00000515242"; exon_number "1"; gene_name "DDX11L1"; gene_biotype "pseudogene"; transcript_name "DDX11L1-201"; exon_id "ENSE00002234632";
chr1	transcribed_unprocessed_pseudogene	exon	12613	12721	.	+	.	gene_id "ENSG000002