...

• Forward – Forward: Both ends of the read are matching the strand of the transcript. Generally colorspace data generated from SOLiD technology would follow this format

...

Depending on the annotation file, the output could be one or two data nodes. If the annotation file only contains one level of information, e.g. miRNA annotation file, you will only get one output data node. On the other hand, if the annotation file contains gene level and transcript level information, such as those from the Ensembl database, both gene and transcript level data nodes will be generated. If two nodes are generated, the Task report will also contain two tabs, reporting quantification results from each node. Each report has two tables. The first one is a summary table displaying the coverage information for each sample quantified against the specified transcriptome annotation (Figure 4).

The second table contains feature distribution information on each sample and across all the samples, number of features in the annotation model is displayed on the table title (Figure 5).

...

• Percentage of the features within the read count range

The coverage breakdown bar chart is a graphical representation of the reads summary table for each sample (Figure 7)

In the box-whisker plot, each box is a sample on X-axis, the box represents 25th and 75th percentile, the whiskers represent 10th and 90th percentile, Y-axis represents the read counts, when you hover over each box, detailed sample information is displayed (Figure 8).

...

There are two parameters in Quantify to reference (Figure 12):

...