Key Output Files and Metrics

Navigate to the completed analysis run to review the results.

Results files per sample can be found within the analysis.

Key Output Files

To learn more about key 5-Base specific output files, reference the DRAGEN documentation: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-methylation-pipeline/dragen-5base-pipeline#methylation-calling-outputs

To learn more about non-5-Base specific output files, reference the DRAGEN DNA Pipeline documentation: https://help.dragen.illumina.com/product-guide/dragen-v4.4/dragen-dna-pipeline

Where to Start when Reviewing QC

A positive (pUC19) and negative (lambda) control genome are spiked-in to each sample during library prep. Neither control is fully methylated/unmethylated, but the pUC19 control should have over 90% methylation, and the lambda control should have under 1.5% methylation. To check the methylation for these controls, review the DRAGEN Report and navigate to the Methylation tab, and then the Context QC table. The "% of CpG" column reflects the % methylation of these controls.

CX Report

The *CX_report file will be generated for all analyses. It will have the following format:

• Each line = 1 cytosine in reference genome (with non-zero coverage)​

• # reads can be dedup’d or not, depending on analysis settings (we use dedupping)​

• mC=methylated, C=unmethylated support​

• Overall methylation level = mC_reads / (mC_reads + C_reads)​

• Overall coverage (STRANDED) = mC_reads + C_reads