Guide RNA Library Data Analysis

A Matlab app for analysing fastq.gz files from Nanopore Sequencing.

Step 1. Place this app within the same folder as the sequencing data folders. Prepare the excel file "Samples.xlsx" stating the sample informations. The input format should be followed:

First column: Sample name

Second column: Foldername or Barcodes from SQK-RBK110.96, it should contain a series of fastq.gz files. Run this Matlab app.

Prepare the spacer information in Excel file, where first three column could be user-specific information, with fourth column as spacer sequence. The spacer Excel file name should be entered in the "Settings" tab.

Step 2. Go to the 'Main' Tab and change the 'Locator Sequence', 'Original Plasmid Sequence' and the 'Placeholder Sequence'.

- The Locator Sequence should be 20bp upstream of the gRNA sequence.

Step 3. Click 'Process reads', and the gRNA analysis will start, monitor the message box below to see the progress.

Step 4. An Excelsheet named 'results.xlsx' will be produced. Go over to "Analysis" tab to choose the sample and plot graph to obtain some preliminary results.

Step 5 (Optional). To identify more reads, homopolymer compression is used to recover reads from the same sample. It will also export the data to the 'results.xlsx'.