Software and scripts required
Make sure the following software is installed: FastQC, Trim Galore, STAR, HTSeq, 
R, edgeR, RSeQC, Piccard Tools, samtools. 

The python main script calls other scripts, make sure they are available from 
the $PATH: functions.py, analysis_info.py, organizeWorkingDirectory.py, qcReads.py, 
trimmingReads.py, fastqc_tables_all.py, mappingReads.py, mappingQC.py, mapping_summary.R, 
mapping_distribution.R, junctionPlotAll.R, countingReads.py, countsLog_rnaseq.R.

Note: some scripts are called from ~/bin, which means a copy should be stored there, (to-do: fix this):
•	RSeQC scripts: junction_annotation.py, junction_saturation.py, gene body coverage.py
•	junctionPlotAll.R

##------------------------------------------------------------------------------##

# Download and Install
----------------------
 $ git clone https://github.com/CGSbioinfo/RNASeq_pipeline.git

 $ cd RNASeq_pipeline/scripts
 $ for i in $(ls *); do cp $i /usr/local/bin; done # NEED SUDO!!
 $ for i in $(ls *); do chmod 777 /usr/local/bin/$i; done # NEED SUDO!
 $ cp junctionPlotAll.R ~/bin 

##------------------------------------------------------------------------------##

# Running the pipeline

Setting up the analysis
-----------------------
1.	Go to the main folder of the project and run:
    		$ analysis_info.py
This will create a file named analysis_info.txt, which needs to be filled in a text editor.
2.	Create a sample_names.txt file with the list of the sample names
3.	Next run:
    		$ organizeWorkingDirectory.py --analysis_info_file analysis_info.txt

QC and trimming
---------------
Run the following commands:
  $ qcReads.py --in_dir rawReads/ --out_dir rawReads/
  $ fastqc_tables_all.py --in_dir rawReads/ --out_dir rawReads/ --suffix_name _raw --out_dir_plots Report/figure/rawQC --readType pairedEnd 
  $ trimmingReads.py --in_dir rawReads/ --out_dir trimmedReads/
  $ fastqc_tables_all.py --in_dir trimmedReads/ --out_dir trimmedReads/ --suffix_name _trimmed --out_dir_plots Report/figure/trimmedQC --readType pairedEnd

Mapping and mapping QC
----------------------
Run the following commands:
  $ mappingReads.py --in_dir trimmedReads/ --out_dir alignedReads/
  $ mappingQC.py --in_dir alignedReads/ --out_dir alignedReads/QC/ --out_dir_plots Report/figure

Counting Reads
--------------
Run the following commands:
  $ countingReads.py --in_dir alignedReads/ --out_dir alignedReads/ --mapping_summary_file mapping_summary.csv