Output from Analyze QIAseq Methyl
The following outputs are generated:
- Genome browser view (
): Collection of output tracks, allowing multiple data types at the same genomic position to be viewed simultaneously. Note that not all output tracks are necessarily in the browser. Tracks can be added and removed from the browser.
- Sample report (
): Sample report containing essential information from all reports produced by the workflow.
- QC & Reports folder:
- Coverage report raw reads (
): Summarizes coverage statistics for mapped raw reads in target regions. The report is based on extended target regions and provides QC for on-target mapping specificity.
- Coverage report UMI reads (): Summarizes coverage statistics for mapped UMI reads in target regions. The report assesses whether the sample has sufficient coverage for variant detection.
- Initial mapping report (): Summarizes and visualizes various mapping statistics from Map Bisulfite Reads to Reference.
- Initial sequence QC report (): Summarizes and visualizes various statistics of the input reads.
- Methylation report (): Summarizes various statistics for the methylation level calls.
- Remove and annotate UMI report (): Summarizes the identified UMIs.
- Remove ligation artifacts report (): Summarizes ligation artifacts found in and removed from the read mapping.
- Trim reads report (): Summarizes the performed read trimming
- UMI groups report (): Summarizes the UMI groups.
- UMI reads report (): Summarizes the UMI reads.
Note that data generated with QIAseq Targeted Methyl Panels uses 'NNCNNCNNCNN' UMIs, which results in a higher percentage of the C nucleotide in the 'Nucleotide percentages of the unique molecular barcode symbols' plot.
- Additionally, if running methylation profile prediction:
- Methylation profile report (): Shows the percentage of the sample estimated to come from epithelial cells (Epi), fibroblast cells (Fib), and immune cells (IC). See Predict Methylation Profile for details.
- Methylation profile report (
- Coverage report raw reads (
- Tracks folder:
- Mapped UMI reads (
): Read mapping from Map Bisulfite Reads to Reference after additional UMI collapsing, see Calculate Unique Molecular Index Groups and Create UMI Reads from Grouped Reads for details.
- Methylation levels (
): Information about methylated and unmethylated cytosines.
- Per-region statistics track (): Coverage statistics for each target region.
- Additionally, if running methylation profile prediction:
- Methylation profile (): Predicted sample composition. See Predict Methylation Profile for details.
- Methylation profile (
- Mapped UMI reads (
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The provided methylation reference database (Homo_sapiens_CpG_hg19_EpiFibIC) in Predict Methylation Profile is constructed from a limited set of epithelial, fibroblast, and immune cell types. It is possible that the epithelial, fibroblast, and immune cell types in any given sample differ from these, and have different methylation profiles. If this is the case, then prediction performance may suffer.
We advise testing the database on pure samples and mixtures with known proportions to see if it is suitable for the analysis.
If it is necessary to create a database, use the tool described in Create Methylation Database. |