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  • SNP discovey in 454 (RNA-seq) data

    Hi All,

    I've a query regarding mutation analysis on 454 RNA data.I've RNA of specific human gene, say PRMT5 (isolated from 100 individuals,pooled and sequenced in 454) of avg read length 400bp.

    I used BWA to map reads to mRNA sequence and used GATK for variant calls, but it did not detect any variants. the coverage was ~ 3000x. We're expecting few variants on the sample, but don't know the optimal pipeline for this.

    I want to know:
    1) Optimal strategy and combination of tools (for mapping, SNP calling, annotation for 454 RNA-seq) to use to achieve this?
    2) Do I used mRNA or chromosome sequence to map against? I want to annotate SNPs at later stage.
    3) Since this is a pooled sample, is duplicate removal recommended?

    Look forward to any suggestions and guidelines

    Thanks

    Raj

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