An example using Illumina barcoded sequences

The data set in this example can be found at the Short Read Archive at NCBI. Use the Search for Reads in SRA... tool to search for SRX014012. Select the SRR03730 item and click Download Reads and Metadata. Save the sequence list in the Navigation Area, and use it with the Demultiplex Reads tool.

The barcoding was done using the following tags at the beginning of each read: CCT, AAT, GGT, CGT (see supplementary material of Cronn2008). The settings in the dialog should thus be as shown in figure 21.29.

Image illumina_barcoding_step2
Figure 21.29: Setting the barcode length at three.

Click next to the "Set barcode options" dialog and use the Add button) to specify the bar codes as shown in figure 21.30.

Image illumina_barcoding_step3
Figure 21.30: A preview of the result

With this data set we got the four groups as expected (shown in figure 21.31). The Not grouped list contains 445,560 reads that will have to be discarded since they do not have any of the barcodes.

Image illumina_barcoding_result
Figure 21.31: The result is one sequence list per barcode and a list with the remainders