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Min Read Count
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This column allows users to set custom minimum read count thresholds for different targets.
If the value is specified as Use Global
Value for a target (the value in the row) in
this column, then the global minimum read count threshold is
used. (For example: 20 reads or 40 reads for Fusions as set
using the minimum read count for Fusions parameter.) If a user
changes the value for any target from Use Global
Value to an allowed integer value (for example:
50), then that value overrides the global threshold. The new
threshold (50 in this example) is used to call that target as
Present/Absent. All other targets will still use the global
threshold. This column overrides these global parameters at the
individual target level (minimum read count for Fusions, minimum
read count for Controls, minimum read count for Gene Expression,
minimum read count for Non-Targeted fusions). This property is
not applicable to 5p3pAssay type targets.
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Min Normalized read count
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This column allows users to set custom minimum normalized read count thresholds for
different targets. If the value is specified as Use
Global Value for a target (the value in the row)
in this column, then the global minimum read count threshold is
used. (For example : 0.0 or 0.0015 reads for Fusions.) If a user
changes the value for any target from Use Global
Value to an allowed value (for example : 0.1) ,
then it overrides the global threshold and the new threshold
(0.1 in this example) is used to call the target as
Present/Absent. This column can be used to override the minimum
normalized read count global parameters at individual target.
This property is not applicable to 5p3pAssay type targets.
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Make Calls
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This column allows users to enable making Present/Absent call for RNAExonVariants at
individual target level. This property is not applicable to any
other type. By default the analysis workflow parameters are set
to not make calls for all the RNAExonVariants. If the value for
any RNAExonVariant target (the value in the row) is changed from
Use Global value to
True, the target will be called
Present/Absent based on the read count and wild type ratio.
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Min WT Ratio
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This column allows users to set custom threshold for minimum wild type ratio for RNAExonVariants at individual target level.
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Do Not Report
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By changing the value to True for any target, that target is not
displayed in the output files and reports.
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Max Read Count Negative
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This column allows users to set nocall range for any fusion target. The value specified in this column should be always less than or equal to the value for minimum read count as set by global parameter threshold or custom threshold for that target.
For example, if a global threshold for minimum read count for fusion is 40, and
Max Read Count Negative is set to 20 for a target (T1)_ , if the count of target T1 is between 20 and 40, it will be called as nocall. If the count is <20, it is called as absent; if it is >40 it is called as present.
This is not applicable to 5p3pAssay type targets.
If the value for Max Read count Negative is equal to the min read
count for any target, then the target is called Absent; if the
read count is less than that value, it is called as Present.
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Minimum Imbalance Score for the RNAExon Tile Assays
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Minimum imbalance score for calling imbalance positive from RNA exon
tiling assays in a driver gene. Positive calls also depend on
p-value for imbalance.
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Maximum p-value for Imbalance for the RNAExon Tile Assays
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Maximum statistical significance p-value for calling imbalance
positive from RNA exon tiling in a driver gene.
Positive calls also depend on imbalance scores.
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Minimum average read counts from all the Exon Tiling
assays in a Driver Gene to proceed with Imbalance
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Mean coverage of a driver gene with RNA exon tiling assays. Measured per gene, as the total valid mapped reads counts from all exon-tiling assays divided by the number of exon-tiling assays.
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Max Weak
Amplicons
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Maximum number of failed amplicons that are allowed beyond breakpoint. The RNA Exon
Tiling amplicons beyond the breakpoint are required to have
sufficient expression. The parameter defines an upper bound to
allowed number of Exon Tiling amplicons that fail to reach a
coverage threshold. (Coverage that is below than 20x coverage
the maximal amplicon in the gene.)
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Min Flank
Amplicons
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Minimum number of flanking amplicons for predicted RNAExonTile breakpoint. The breakpoint
predicted by the RNA Exon Tiling algorithm should be flanked by
a minimal number of amplicons – defined by the parameter – on
both sides. This setting will exclude breakpoint prediction
occurring at the 3’ or 5’ end of the genes.
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