BAM Input Engine

Running this process using the GSE18905_2MUS_chrY example generates the Results window shown below. Refer to the BAM Input Engine process description for more information.

The Results window contains the following elements:

Output Data

This process generates the following data sets:

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Experimental Design Data Set (EDDS): This data set lists specific information about experimental details for each of the arrays. Refer to Experimental Design Data Set (EDDS) for more information about this data set. Note: In addition to the columns normally found in an EDDS, this data set contains a new TotalReads column.

•	Count Summary Data Set: This data set lists chromosome and positional information and whether the sample sequences match the reference sequence (indicated with the appropriate read/count measure) or diverges from the reference sequence (indicated with a “.”) at each position.

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Output Annotation Data Set: This data set lists on the information biological or chemical properties, such as gene identity or chromosomal location, for each of the markers/ molecular entities in the experiment. Refer to Annotation Data Sets for more information about this data set. Note: This data set is generated only when an Annotation File is specified.

•	RPKM Summary Data Set: This data set lists the reads per kilobase of the transcript per million mapped reads to the transcriptome.

•	RPM Summary Data Set: This data set lists the reads per transcript per million mapped reads to the transcriptome.

Note: If you chose Exon as the Summarization Method, this process determined the exon-exon junction level counts. This calculation does not necessarily include position or physical distance measurements. Because neither RPKM nor RPM can be determined without specifying the length of the feature, neither the RPKM nor the RPM data sets are generated.

Note: You can view the data in a file or data set by clicking either Open or View Subset (when the data set is very large).

Launch Follow-up Processes

•	Basic RNA-Seq Workflow: Click Basic RNA-Seq Workflow to launch the Basic RNA-Seq Workflow process with the Count Summary data set and EDDS specified as input.

•	Basic miRNA/RNA-Seq Workflow: Click Basic miRNA/RNA-Seq Workflow to launch the Basic miRNA/miRNA-Seq Workflow process with the Count Summary data set and EDDS specified as input.

•	Gene Model Summary: Click Gene Model Summary to launch the Gene Model Summary process with the Count Summary data set specified as input.

•	RPM Scaling: Click RPM Scaling to launch the RPM Scaling process with the Count Summary data set and EDDS specified as input.

•	Upper Quartile Scaling: Click Upper Quartile Scaling to launch the Upper Quartile Scaling process with the Count Summary data set and EDDS specified as input.

•	TMM Normalization: Click TMM Normalization to launch the TMM Normalization process with the Count Summary data set and EDDS specified as input.

•	KDMM Normalization: Click KDMM Normalization to launch the KDMM Normalization process with the Count Summary data set and EDDS specified as input.

General

•	Click Reopen Dialog to reopen the completed process dialog used to generate this output.

•	Click Close All to close all graphics windows and underlying data sets associated with the output.