small-RNA Expression Analysis Pipeline

Expression analysis of cellular and plasma micro RNA

The following pipeline allows you to trim small RNA reads generated from Qia-Seq protocol.Reads are then aligned using very sensitive settings in Bowtie2 and counted using GenomicRanges. Differential gene expression analysis using edgeR.

Step1: Trim files one by one using the following command:

sbatch -p gpu --gres=gpu:1 --mem=10g --time=2:00:00 small_RNA_trimming.sh Input_Fastq_Prefix

Step2: Generate the targets file, data, and results directory as described in systemPipeR

Step3: Run small_RNA_alignment.R line by line

Step4: Run small_RNA_readcounting.R line by line

Step5: Run small_RNA_edgeR.R line by line