Ngs MergeNgsSummaryFiles.pdf

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Merge Summary Files

The Merge Summary Files module merges multiple fusion summary files together. This module allows for merging batches of summaries files into a single report.

MergeNGSSumFile1.png

General

Under the "General" tab, the user first has to select and add the summary files. The "Summary type" acceptable include "Mutation", "SNP", "Paired end fusion", "Single end fusion" and QC summary files.

Options

  • Merge into a table report - Allows the user to merge the data into an Array Studio "Table" and optionally apply a name to that table.
  • Merge into a text file - Allows the user to merge the data into a text file the will be saved locally as specified by the user.
  • Genome - used for mapping and must be selected (include any genome model where an index has already been built, and allows the user to build one on the fly for a new Genome model).
  • Gene model - used for mapping and must be selected (include any gene model where an index has already been built, and allows the user to build one on the fly for a new Gene model).
  • Exclude fusion if unique position #< - The minimal number of hits for a particular fusion to be reported. The default value = 2.
  • Report unannotated fusion - When selected, this will report fusion regions that have no gene annotation information.

Fusion Filtering

In the Filtering Tab the user have various options for filtering gene family lists as shown below.

MergeNGSSumFile2.png

  • Filter by default gene blacklist and gene family list - see http://www.omicsoft.com/downloads/fusion/filtering/ for the default genes that will be excluded. Gene family defines sets of genes that, if the fusion occurs within the same gene family, it will be skipped.
  • Filter by customized gene blacklist and gene family list - same as above but it can be customized using the instructions in the window.
  • No filtering

Results

The resulting dataset will contain the merged summary table that will either be located in the "Table" section of the Solution Explorer, or a locally saved text file depending on the option selected.

MergeNGSSumFile3.png

OmicScript

MergeNgsSummaryFiles