MiSeq was designed to have minimum "user serviceable" parts (including software to run it) and this is a side effect of that convenience. In the process of simplifying the user interface they had to change several things. For most users this is the preferred solution so in general it works fine. Only in cases such as what you saw additional work is needed at times.
Since there is no phasing information available for the last base in tag that base is not considered during demultiplexing. One can use "--use-bases-mask" creatively but using a samplesheet with (n-1) bases works.
I assume you are re-running the de-multiplexing with the correct samplesheet and will let us know what happens.
Since there is no phasing information available for the last base in tag that base is not considered during demultiplexing. One can use "--use-bases-mask" creatively but using a samplesheet with (n-1) bases works.
I assume you are re-running the de-multiplexing with the correct samplesheet and will let us know what happens.
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