Modifying the Block CNV report
The dialog box has two tabs, Advanced Settings and Report Settings. After you modify the settings, and then click OK, the report display is dynamically updated.
 | After you made your edits, you can click Save Settings to save the settings for this report in a Settings file (.ini file), which can be used to generate the Block CNV report for another project based on the settings in the file. |
Setting | Description |
|---|---|
Advanced Settings | |
Ignore up to [0] regions when merging | If there are “n” number of regions that are reported as normal within a larger number of regions that show the same CNV, then these normal regions are ignored and the regions with the same CNV are merged to create blocks. Note: Uncalled regions are automatically ignored. |
Hide unplaced/unlocalized contigs | Exclude unplaced/unlocalized contigs from the report. |
Report Settings | |
Index | An ordered count of the segments that are used in the report. |
Chr • Name • Number | • The name of the chromosome on which the segment is located. • The number of the chromosome on which the segment is located. |
Chr Position Start | The base number that indicates where the segment starts in the chromosome. |
Chr Position End | The ending base number that indicates where the segment ends in the chromosome. |
Gene | The gene name for the segment when the segment is the whole gene or the name of the gene on which the segment is found. |
Exon | The exon number for the segment location. |
Number of Regions | The number of consecutive regions that have a CNV and, as a result, were grouped together. |
RNA Accession | Available only for the CNV report. |
Protein Accession | Available only for the CNV report. |
Description | Available if the reference file is a .fasta file with multiple segments. Select this option to display the title line for each segment in the Description column. |
Contig | The contig on which the segment is located. The contig is based on the genome assembly from the NCBI. |
Locus Tag | Available only for the CNV report. |
Start | The starting location for the reference region. |
End | The ending location for the reference region. |
Length | The total length of the reference region, which provides for easy identification of expressed regions by size (such as when locating small RNA transcripts). |
Original Coverage | Available only for CNV report. |
Dispersion | The dispersion value for the region. N/A for Uncalled regions. |
Normalized Coverage | Available only for CNV report. |
The following two Display settings are available only if RPKM is selected. | |
Ratio | The ratio of the sample RPKM to total RPKM for the region |
Total RPKM | The sum of the Sample RPKM and the Control RPKM. |
The following two Display settings are available only if Normalized Counts is selected. | |
Ratio | The ratio of the sample RPKM to total RPKM for the region. |
Total Read Counts | The sum of the Sample read counts and the Control read counts. |
Report Settings - Filter Settings | |
Display Deletion | Selected by default. Show CNVs that are classified as Deletions. Clear this option to hide this classification from the CNV Tool report. |
Display Normal | Selected by default. Show regions that are classified as Normal (little evidence of a CNV). Clear this option to hide this classification from the CVN Tool report. |
Display Duplication | Selected by default. Show CNVs that are classified as Duplications. Clear this option to hide this classification from the CNV Tool report. |
Median Deletion Score > 1.000 | The median deletion threshold across all the regions in the block for the block to be included in the report. |
Max Deletion Score > 1.000 | The maximum deletion threshold across all the regions in the block for the block to be included in the report. |
Median Duplication Score > 1.000 | The median duplication threshold across all the regions in the block for the block to be included in the report. |
Max Duplication Score > 1.000 | The maximum duplication threshold across all the regions in the block for the block to be included in the report. |
In BED region | Not available if a BED was loaded on the Basic Settings tab for the CNV Tool. Filters the Block CNV report to include only those regions that are contained in the BED file. Click Set to browse to and select the appropriate BED file. Note: A BED file is a tab-delimited text file. You can upload a BED file only if the reference sequence contains chromosome information, which means that the reference sequence must be either a preloaded reference that NextGENe supplies, or a GenBank reference file that contains chromosome information. |