Open Arabidopsis Thaliana, 2009
Zoom to 2,258,737 : 2,258,850 on chromosome
Load [CoolHT2.sm.bam
http://www.transvar.org/illumina/tophat-1.1.4-heat-drought-processed/CoolHT2.sm.bam\
]
Refresh for 'Region in View'. All the reads should appear as sequence.
Hit 'Load Sequence in View' button. After sequence loads, all sequences should flip to solid color with only mismatches showing.
Right click one read; choose "Show aligned sequence". The individual read should now show the full sequence.
Use the mouse to select several reads. Right click within the group, choose "Show aligned sequence". All selected reads should now show the full sequence.
Select some reads showing the sequence, right click, choose "Show mismatches only" and be sure they change back to solid bars with only mismatches showing.
Test Results
December 17, 2010 - Alyssa Gulledge

version 6.5 (7251). Tested this out. The initial tracks show as sequence, then convert to mismatches only when genomic sequence is loaded. Individual reads readily convert back and forth from the right-click menu. However, selecting a group of reads and then right clicking within that group drops the group select, and ONLY selects the read under the mouse - so groups of reads cannot be changed all at once...