Defining reference genome and mapping settings

You are now presented with the dialog shown in figure 27.4.

Image mrna_seq_step2
Figure 27.4: Defining a reference genome for RNA-Seq.

At the top, there are two options concerning how the reference sequences are annotated:

Just below these two options, you click to select the reference sequences.

Next, you can choose to extend the region around the gene to include more of the genomic sequence by changing the value in Flanking upstream/downstream residues. This also means that you are able to look for new exons before or after the known exons (see Exon discovery).

When the reference has been defined, click Next and you are presented with the dialog shown in figure 27.5.

Image mrna_seq_step2b
Figure 27.5: Defining mapping parameters for RNA-Seq.

The mapping parameters are:

There is also a checkbox to Use color space which is enabled if you have imported a data set from a SOLiD platform containing color space information. Note that color space data is always treated as long reads, regardless of the read length.