While visualizing my alignments on IGV, I noticed that some of the reads contain mismatches at the 3’ end. Is there a way to generate an alignment file with the mismatches removed? Thanks!
Hi @cjain,
The question is not related to Galaxy, but I googled it:
Go to View > Preferences (or right-click directly on the alignment track). Under the Alignments tab disable “Show mismatched bases” option.
Does it work for you?
Kind regards,
Igor