Summarization Method

For the SAM, BAM, and Eland Input Engines:

For Gene Model Summary:

For the SAM, BAM, and Eland Input Engines:

Select a way to summarize the reads.

Choices are described below.

Summarization Method	Description	Annotation File required?	Columns added to output EDF
Fixed Bin Size	Summarize reads based on equal-sized bins . Specify the size of each bin in the Bin Size field.	No	TotalReads
Exon	Summarize reads based on exons . Note : Exon-exon junction counts are included. For example, a read overlapping both exon1 and exon2 is shown as 1_2 in the exon column of the output summary data sets. Starting with the reads data file , the position of each read is compared with exon start and end positions so that each read is assigned an exon membership. Count data is then summarized based on exons.	Yes Important : Feature Identifier s must be unique in order to assign unique identifiers to exons.	TotalReads TotalCounts CountPerRead
Gene(s)	Summarize reads based on their alignment within known or predicted transcribed sequences . Starting with the reads data file , the position of each read is compared with start and end positions so that each read is assigned a gene membership. Count data is then summarized based on genes. Note : “Gene” is defined broadly in this case. Because information about which strand corresponds to the reads is lacking, a “gene” could include one or more genes that either overlap or lie adjacent to each other either on the same or on opposite strands.	Yes Important : Feature Identifier s must be unique in order to assign unique identifiers to genes.	TotalReads TotalCounts CountPerRead

To Specify a Summarization Method:

Click the radio button corresponding to a summarization method.