I generally never use the --use-bases-mask so I will defer to HESmith's expertise.
Dropping the --use-bases-mask altogether and using a samplesheet with 7bp indexes should work as well. That should produce three files: R1 - First read, R2- Second tag or whatever is there, R3 - Should be the real read 2. When the edited RunInfo.xml file is used.
Dropping the --use-bases-mask altogether and using a samplesheet with 7bp indexes should work as well. That should produce three files: R1 - First read, R2- Second tag or whatever is there, R3 - Should be the real read 2. When the edited RunInfo.xml file is used.
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