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Coverage report is also available for data nodes containing aligned reads (either Aligned reads or Trimmed reads). The purpose of the report is to understand how well the genomic regions of interest are covered by sequencing reads for a particular analysis.
When setting up the task (Figure 1), you first need to specify the Genome build and then a Gene/feature annotation file, which defines the genomic regions you are interested in (e.g. exome or genes within a panel). The Gene/feature annotation can be previously associated with Partek® Flow® via Library file management or added on the fly.
Complete coverage report will contain percentage of bases within the specified genes / features with coverage greater than or equal to the coverage levels defined under Add minimum coverage levels. To add a level, click on the green plus. Alternatively, to remove it, click on the red cross icon.
As for the Advanced options, if Strand-specificity is turned on, only reads which match the strand of a given region will be considered for that region’s coverage statistics. Generate target enrichment graphs will generate a graphical overview of coverage across each feature.
Region name: the genomic feature identifier (as specified in the annotation file)
Chromosome: the chromosome of the genomic feature (or region)
Start: the start position of the genomic feature (1-based)
Stop: the stop position of the genomic feature (2-based, which means the stop position is exclusive)
Strand: the strand of the genomic feature
Total exon length: the length of the genomic feature
Reads: the total number of reads aligning to the genomic feature
% GC: the percentage of GC contents of those reads aligning to the genomic feature
% N: the percentage of ambiguous bases (N) of those reads aligning to the genomic feature
(n)x: the proportion of the genomic feature which is covered by at least n number of alignments. [Note: n is the coverage level that you specified when submitting Coverage report task, defaults are 1×, 20×, 100×]
Average coverage: the average sequencing depth across all bases in the genomic feature
Average quality: the average quality score across covered bases in the genomic feature
: the invokes the Coverage graph across the genomic feature, showing the current sample only (Figure 23) (or mouse over to get a preview of the plot)
: the invokes the Chromosome view and browses to the genomic location
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