After SplitNCigarReads, does the separated reads both labeled as primary alignment?

jzhongzyjzhongzy Phoenix,AZMember

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?



  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @jzhongzy

    SplitNCigarReads will create a primary alignment from the left-most part of the read, and supplementary alignments (not secondary) from the remaining parts. SplitNCigarReads will ignore secondary alignments unless you pass
    --process-secondary-alignments true
    . Since specification of primary vs supplementary alignments is somewhat arbitrary for chimeric reads, downstream tools should treat all the reads equally.

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