How can I view the bases for mapped reads that extend beyond the end of a reference sequence?
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This information does not pertain to track-based objects.
For reads that map at the end of a reference sequence, any section of the read extending beyond the end of the reference sequence will be not visible. The existence of read information extending beyond the end of reference sequence is indicated by an arrow (>). The steps you need to take to be able to view the bases in such unaligned read ends are:
Editing your reference sequence If you wished to add a series of Ns to the start of a reference sequence, then you would:
To add Ns at the othe end of the reference, just select the last base of the reference and repeat the above actions.
Working with mappings with extended reference sequences After mapping to your edited reference, the ends of any reads extending into the area with the Ns, will be considered non-matching, and therefore appear in faded colours. If no un-mapped ends appear then please make sure that you have selected to show the sequence ends in the side panel. To get the consensus sequence for such regions, you need to manually drag the end point for each read to be considered. To do this:
All read ends that you want to include in the consensus (or contig) calculation should be dragged to include them in the mapping in the above manner. The consensus sequence will appear after you have released the mouse button after dragging.
Additional information about viewing options for mappings If you select the compactness view called Packed in the side panel and then choose to Show mismatches, the nucleotides are colored in a way that may make it easier for your to get an idea about how well the consensus is representing your reads. Alternatively, if you want to include all reads, but without viewing the quality scores, you may wish to try the compactness view called Low. You can find further details about viewing options for read mappings in our manual here: CLC Main Workbench: |