When using qAlign in QuasR package and set parameter to splicedAlignment=TRUE, what happen with the continuous (unspliced) reads. Are they completely removed from the alignment?
No, you get those reads as well.
When you use splicedAlignment=TRUE, you should get more or less the same number of 'unspliced' alignments (as if you use splicedAlignment=FALSE) plus the extra 'spliced' alignments.
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