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#!/usr/bin/env python
import pyBigWig
import argparse
import os.path
import sys

parser = argparse.ArgumentParser(description="Subset a single chromosome from a bigWig file.")
parser.add_argument("--headerToo", action="store_true", help="Subset the header too, which can expedite some downstream programs but possibly cause problems for others.")
parser.add_argument("input", help="Input bigWig file.")
parser.add_argument("output", help="Output bigWig file.")

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source("https://raw.githubusercontent.com/venuthatikonda/rFun/master/plotSE.R")

# Example 1 - defaults

plotSE(seFile="example_AllEnhancers.table.txt", seCol = "red", teCol = "black", mark = "H3K27ac", bg=TRUE)+ggtitle("Example - 1")

# Example 2 - differnet colors

plotSE(seFile="example_AllEnhancers.table.txt", seCol = "deeppink", teCol = "darkgreen")+ggtitle("Example - 2")

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plotSE<-function(seFile, seCol="red", teCol="black", mark="H3K27ac", bg=TRUE){
  
  dat=read.delim(seFile, comment.char = '&', nrows=3)
  colnames(dat)<-"V1"
  se.signal.cut=as.character(dat$V1[3])
  se.signal.cut=as.numeric(strsplit(se.signal.cut, " ")[[1]][4])
  
  se=read.delim(seFile, comment.char = '#', header = TRUE)
  se.count.cut=dim(subset(se, se$isSuper==1))[1]
  

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Command executed

python coltron-1.0.2/coltron/crc.py -e MB12_H3K27ac_peaks_noEncBlack_AllEnhancers.table.txt -b tumor_MB12_H3K27ac_CAGATC_merged.rmdup_sub.bam -g HG19 -n MB12 -o MB12/

Following errors were occurred

Error - bamliquidator_batch

itsvenu

Tool	Use	Link
Chip enrich	Functional enrichment of ChIP enriched regions	http://chip-enrich.med.umich.edu/chipMain.jsp
REDItools	RNA editing detection	https://www.ncbi.nlm.nih.gov/pubmed/23742983
Screw	Single-cell epigenomics workflow	https://github.com/Epigenomics-Screw/Screw
Google classroom	Handy teaching tool	https://classroom.google.com/h
Piazza QA platform	Free Q&A platform	https://piazza.com/
Latex slides	Easy to edit slides (best for teaching)	https://www.overleaf.com/gallery/tagged/presentation#.WXMl9tOGP6Y
Moodle	Create your own course	https://moodle.org/?lang=nn
MultiQC	NGS data QC tool	http://multiqc.info/

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# load required libraries
library(shiny)
library(plyr)
library(ggplot2)
library(googleVis)
library(reshape2)


####creation of example data on local directory for uploading####

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##

library(limma)
library(illuminaHumanv4.db)

args=commandArgs(TRUE)
sam=read.ilmn(args[1],ctrlfiles=args[2],other.columns="Detection")

# Normalization - neqc

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#!/usr/bin/perl -w

my $columns = 60;


my $progname = $0;
$progname =~ s/^.*?([^\/]+)$/$1/;

my $usage = "Usage: $progname [<Stockholm file(s)>]\n";
$usage .=   "             [-h] print this help message\n";