Output from the Detect QIAseq Methylation workflow
The following outputs are generated:
- Genome Browser View (
): A 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 as described in https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Track_lists.html.
- Sample report (
): A report containing essential information from all reports produced by the workflow. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Create_Sample_Report_output.html for details.
- QC & Reports folder:
- Initial mapping report (
): Summarizes and visualizes various mapping statistics from Map Bisulfite Reads to Reference. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Summary_mapping_report.html for details.
- Initial sequence QC report (): Summarizes and visualizes various statistics of the input reads.
See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=QC_Sequencing_Reads.html for details.
- Methylation profile report (), if running methylation profile prediction: 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 report (): Summarizes various statistics for the methylation level calls. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Call_Methylation_Levels.html for details.
- Remove and annotate UMI report (): Summarizes the identified UMIs. See Remove and Annotate with Unique Molecular Index for details.
- Target coverage report (): Summarizes various coverage statistics for the target regions. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Coverage_summary_report.html for details.
- Trimmed reads report (): Summarizes the performed trimming. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Trim_output.html for details.
- UMI group creation report (): Summarizes the UMI reads. See Create UMI Reads from Grouped Reads for details.
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.
- UMI group report (): Summarizes the identified UMI groups. See Calculate Unique Molecular Index Groups for details.
- Initial mapping report (
- Tracks folder:
- Final UMI read mapping (
). Read mapping from Map Bisulfite Reads to Reference after additional UMI collapsing. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Map_Bisulfite_Reads_Reference.html, Calculate Unique Molecular Index Groups, and Create UMI Reads from Grouped Reads for details.
- Methylation levels (
). Information about methylated and unmethylated cytosines. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Call_Methylation_Levels.html for details.
- Methylation profile (), if running methylation profile prediction. See Predict Methylation Profile for details.
- Target coverage (). Information about coverage for each target region. See https://resources.qiagenbioinformatics.com/manuals/clcgenomicsworkbench/current/index.php?manual=Per_region_statistics.html for details.
- Final UMI read mapping (
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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. |