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How can I choose parameters in STAR to satisfy a read that only matches a position in the genome?

In the downstream analysis of RNA-seq, such as gene expression calculation, SNP calling, Is it necessary that one read must be aligned to a single position in the genome? If so, How can I choose parameters in STAR to satisfy the condition? Thanks :)


  • bhanuGandhambhanuGandham Cambridge MAMember, Administrator, Broadie, Moderator admin

    Hi @Aura

    We recommend using STAR aligner but do not support it. STAR is not a GATK tool. This question might be better suited for or

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