Bulk_RNAseq

Repository for Bulk RNA-seq analysis

Step 1. Import necessary tools

bash preparation.sh

Bulk_RNA_dir
	L---tools
	L---reference														   
			L---Homo_sapiens
				L---star																		
				L---UCSC/hg38											
					L---Sequence/WholeGenomeFasta/genome.fa											
					L---Annotation/Genes/genes.gtf
	L---data
		L---*.bz2 files
			L---STAR_OUTPUT (this directory will be made by running this script)
				L---Sample_output_1
				L---Sample_output_2
				L--- ...
				L---counts

Step 2. Download data

Prepare input file wich has all the ftp addresses of the data you want.
Then run either of the following:
qsub -l os7 -cwd ftp_wget.sh your_input_file.txt
OR
bash ftp_wget.sh your_input_file.txt &

Step 3. Map against reference (Star mapper)

The following command maps data against reference and runs feature-counting tools.
qsub -cwd -l os7 star.sh
First time:

Download reference sequence (from NCBI, DDBJ, EMBL etc.)
Prepare reference indices.

Step 4. Summarise mapping/feature count log info

python star_scripts/summarise_feature_counts.py STAR_OUTPUT/

Step 5. Generate feature counts matrix