Tools

The following need to be installed in order to work properly:

• fastqc - fastq quality checking tool
• STAR - rna-seq alignment tool
• cufflinks - outputs gene structure information from rna-seq reads
• samtools - sort SAM file and output to BAM or SAM

Useful:

• seqtk - convert fastq into fasta
• cuffdiff - compare cufflinks output

Running the Pipeline

Put the inputs (reference fasta and rna-seq read fastq) inside of the inputs folder
Run chmod 755 pipeline.sh in order to give read/execution permissions to others
Run ./pipeline.sh –c in order to clear the outputs of the previous run.
Run ./pipeline.sh or sh pipeline.sh in order to run the pipeline.

Results

The fastqc outputs can be seen in the fastqc_results folder.
The cufflinks results can be seen in the cufflinks_results folder.
The star results will be outputted in the folder that pipeline.sh resides.
This pipeline can take a long time as STAR can take a long time to run especially on large sets of data.

Sample Data

Reference ecoli genome
Sample ecoli data