mbk0asis

# run 'blastn' (-outfmt 5 --> XML outformat)
$ for p in ./*pa.fa; 
do  
blastn -outfmt 5 \
       -query hg_normal_ensembl_cancerGenes_mRNA \
       -subject $p \
       -out $p.blast; 
done 

mbk0asis

# Installing Oracle Java on Ubuntu14.04

$ sudo add-apt-repository ppa:webupd8team/java
$ sudo apt-get update
$ sudo apt-get install oracle-java8-installer
$ sudo apt-get install oracle-java8-set-default
$ java -version

# It will output something like below:
java version “1.7.0_60″ Java(TM) SE Runtime Environment (build 1.7.0_60-b19) 

mbk0asis

#############################################################################################
#
# Cancer Mutation Targeted NGS by Multiplex PCR
# Alignmnet on cDNA using 'Bowtie2'
# Variants analyses using 'GATK'
#
#############################################################################################

# extract cDNA sequences from COSMIC "All_COSMIC_Genes.fasta"

mbk0asis

$ trim_galore *

$ bismark_genome_preparation --bowtie2 /genome/dir/

$ bismark -u 10000 --non_directional --bowtie2 -p 8 path/to/BSgenome/dir/ Read.fq --score_min L,0,-1

# '-u' = optional option, map only randomly chosen 10000 reads


# bismark_methylation_extractor

mbk0asis

# replace 100th character (strings and/or numbers) to "M"
$ sed 's/./M/100' input





###############################
$ awk '{ if ($0 ~ /^>/) { print $0; } \      # if the line starts with ">", print all
else { printf("%s%c%s\n", substr($0, 1, 2), "X", substr($0, 4, length($0))); } }' \    # else

mbk0asis

#!/bin/bash

clear
printf '\n\n # cov2bedGraph_highCpG # \n\n # This will convert .cov files from "bismark_methylation_extractor" into .bedGraph files \n\n # Methylation percent will be calculated in selected windows containing specified number of CpGs \n\n # Change reference genome directory before start'

printf '\n\n\n\n\n\n <><><> Sliding Window Parameters <><><> \n\n'
printf '\n\n >>> Enter window size in bp : \n\n'
read win
printf '\n\n >>> Enter slide size in bp : \n\n'
read slide

mbk0asis

library(DESeq)
library(LSD)
library(ggplot2)
library(gridExtra)
library(RColorBrewer)

# open a count file
setwd('/home/bio1/00-NGS/RNAseq/bov/GSE44023_Chitwood_et_al/DESeq')
setwd('/home/bio1/00-NGS/Cancers/cancer_met_Kyuheum')
countsTable<- read.csv("final.final.csv",row.names=1)

mbk0asis

# installation & prerequites
$ sudo apt-get update
$ sudo apt-get install last r-base r-cran-ggplot2 hdf5-tools \
  texlive texlive-latex-extra default-jre git

# Insert following two lines in .profile
export NANOOK_DIR=/path/to/NanoOK
export PATH=/path/to/NanoOK/bin:$PATH

$ source .profile

mbk0asis

#!/bin/bash

clear
printf "\n *** MULTIPLEX PCR PRIMER GENERATOR ***"
printf "\n\n !!! 'Primer3 & fastx-toolkit' must be installed on the system.\n\n !!! Both FASTA & .param files must be in this directory \n\n !!! Edit parameters (e.g. size, Tm, and etc) before start\n\n "

printf "\n\n Usage : \n    ./mp_primer.sh FASTA PARAMETER \n\n\n Enter to continue... "

read

mbk0asis

#!/bin/bash

printf "\n *** BIS BATCH PRIMER version 2.0 ***"
printf "\n\n !!! 'Primer3 & fastx-toolkit' must be installed on the system.\n\n !!! Edit parameters (e.g. sizes, Tm, and etc) before start\n\n "
printf "\n\n  Usage : \n    ./mp_primer.sh FASTA PARAMETER \n\n"
printf "   >>>  input FASTA = "$1
printf " \n   >>>  parameters  = "$2
printf "\n\n\n  ()()() Running... \n\n"

if [ -f $1 -a -f $2 ]; then