Workflow of MBI4850G Project

This project aimed to reproduce the work of Ibrahim et al., through processing their provided miRNA data https://doi.org/10.1093/ijnp/pyae013

The associated write-up and more detailed workflow is detailed in Report.pdf

Downloading data

The data is located on the SRA database with id SRP489148

Cleaning data

The pipeline I immmitated was the exceRpt smallRNA pipeline

Removing low quality reads (trim.sh)

done with trimmomatic

Remove contaminants (rem_uni.sh/rem_rRNA.sh)

• Used NCBI UniVec sequences, and ARF (R package) reference sequences for rRNA
• Aligned data with bowtie2 and took un-aligned sequences

Align and get counts (align.sh/get_counts.sh)

• Use STAR to align and build index with hg38
• Use subreads to get counts

Find Differential Expression

PCA to remove outliers

DESeq2 to get significantly differentially expressed miRNA