Program to analyse CHIP-seq and RNA-seq data
This program is the final proyect of Bioinformatics and Genomics Analysis subject of the 4th year in the Biochemistry Degree at University of Seville.
To install MARLAU follow these steps:
-
Download the zip file MARLAU.zip to a directory of your choice. The opt directory is recommended.
-
Unzip the file:
unzip MARLAU.zip -
Edit your .bashrc file to add the MARLAU path to PATH.
Open a terminal Ctrl+Alt+T
cd
vim .bashrc or nano .bashrc or gedit .bashrc
add to the end of the filethe MARLAU path
PATH=$PATH:MARLAU_PATH
- Bowtie 2 version 2.2.6
- TopHat v2.1.0
- FastQC v0.11.2
- cufflinks v2.2.1
- merge_cuff_asms v1.0.0
- cuffdiff v2.2.1
- R scripting front-end version 3.2.1 (2015-06-18)
- R version 3.2.1 (2015-06-18) -- "World-Famous Astronaut"
- bowtie version 1.1.2
- samtools version 0.1.18
- macs2 2.1.0.20151222
- PeakAnnotator 1.4
- homer v4.8.3
- R package "cummeRbund"
MARLAU "working_directory" "experiment" "/home/opt/parameter_file_rnaseq.txt" "/home/opt/parameter_file_chipseq.txt"
working_directory (opt directory recommended)
parameter_file_rnaseq.txt and parameter_file_chipseq.txt must be in the working_directory (opt directory recommended)
working_directory: /PATH/TO/WORKING/DIRECTORY (WORKING/DIR_MARLAU/EXPERIMENT_MARLAU)
experiment: EXPERIMENT_NAME
number_of_samples: #
url_genome:
url_annotation:
url_sample_1:
url_sample_X:
labels: con1,cond2,cond3
experimental_design: 2,2,3 (Nº of samples of each condition)
comparisons: 1,2,1,3,2,3 (cond1-cond2, cond1-cond3, cond2-cond3)
threshold: # (fold-change value)
pvalue: #
working_directory: /PATH/TO/WORKING/DIRECTORY (WORKING/DIR_MARLAU/EXPERIMENT_MARLAU)
experiment: EXPERIMENT_NAME
experimental_design: 1,1,2,1 (Nº CHIP cond 1, Nº INPUT cond 1, Nº CHIP cond 2, Nº INPUT cond 2)
url_genome:
url_annotation:
experiment_type: TF (TF for transcription factor or EP for epigenetics marks)
targets_threshold: # (threshold for NDG targets)
url_chip1:
url_chipX:
url_input1:
url_inputX: