Create UMI Reads from Grouped Reads

The tool Create UMI Reads from Grouped Reads generates a single consensus read, called a UMI read, from reads which belong to the same group, as determined by the Calculate Unique Molecular Index Groups tool. The consensus reads are placed in a read mapping at the location of the original reads. Therefore, the output of the tool is a read mapping of generated UMI reads.

Create UMI Reads from Grouped Reads is available under the Tools menu at:

        Tools | Biomedical Genomics Analysis (Image biomedical_folder_closed_16_n_p) | UMI Tools (Image qiaseqv3_folder_open_16_h_p) | Create UMI Reads from Grouped Reads (Image create_umi_from_groups_16_n_p)

In the first dialog (figure 4.4), select a read mapping of the original reads with UMI annotations that was previously handled with the Calculate Unique Molecular Index Groups tool.

Image createsupereads
Figure 4.4: Select a read mapping of the original reads with UMI annotations.

The second dialog of the wizard (figure 4.5) offers the following options:

Image createsupereads2
Figure 4.5: Settings for the Create UMI Reads from Grouped Reads tool.

Click Next to Open or Save the resulting read mapping of UMI reads, i.e., a read mapping of the merged UMI groups. UMI reads are named umi[UMI_ID]_count[UMI_group_size], where UMI_ID is a unique UMI group number, and UMI_group_size is the number of reads that are in that UMI group.

It is also possible to generate a report that will indicate how many reads were ignored and the reason why they were not included in a UMI read.



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