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  • Ion Proton for allele-specific ChIP-seq, RNA-seq

    Hi,

    In our lab we are working with allele-specific ChIP-seqs and RNA-seqs. After standard ChIP-seq or RNA-seq protocol we attribute obtained reads to either parental or maternal genome based on available SNP information (there is on avarage 1 SNP per 300 bp).

    Our department hosts Ion Proton device - and many researchers use it successfully for regular ChIP-seq and RNA-seq experiments.
    I would like to get to know if Ion proton is good enough for my purpose.
    Does anybody have experience with allele-specific sequencing on Ion Proton?
    Is HiSeq2000 better enough to justify paying 2-3 time more for my experiments?

    Best,

    Michal

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