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After SplitNCigarReads, does the separated reads both labeled as primary alignment?
Hi, I am doing RNAseq and use STAR for alignment, I am wondering in such situation, a read overlapping the junction site, when I use the SplitNCigarReads operation, it separate the read to two; for these two separated reads, do they both got relabeled as primary alignment (which make more sense) or still secondary alignment for sequence on the right side?
Thanks a lot?