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.Īlternatively, if you want to include all reads, but without viewing the quality scores, you may wish to try the compactness view called Low.2 Manual for CLC Sequence Viewer Windows, Mac OS X and Linux SeptemThis software is for research purposes only. The consensus sequence will appear after you have released the mouse button after dragging.Īdditional information about viewing options for mappings Keeping the mouse button depressed, for each relevant read, drag to the left to extend the 5 prime end, or to the right to extend the 3' end.Īll 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.Put the selection cursor on the the grey vertical line between the faded and non-faded parts and depress the left mouse button.Please ensure the compactness setting for the mapping is set to "Not compact".To make sure you are, click on the button marked with an arrow and labelled Selection in the top toolbar of the Workbench. Make sure you are working with the Selection cursor.To get the consensus sequence for such regions, you need to manually drag the end point for each read to be considered. If no un-mapped ends appear then please make sure that you have selected to show the sequence ends in the side panel. Working with mappings with extended reference sequencesĪfter 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. To add Ns at the othe end of the reference, just select the last base of the reference and repeat the above actions. Type in at least as many Ns as your reads are long and click the button labelled "OK" to save this change.Right click the highlighted nucleotide and select "Edit Selection" in the menu that appears.Open the reference sequences object and highlight the first nucleotide. If you wished to add a series of Ns to the start of a reference sequence, then you would:
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