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  • Counting the total number of SNPs in a transcript

    Hi,

    I have RNAseq data that has been aligned to reference transcriptome and the aligned bam file is sorted and indexed.

    Using that bam file is it possible to estimate the total number SNPs in every read that has been aligned to reference transcriptome. I mean, for an example, if position 2 has base "A" in reference transcript and 20 reads aligned to that region region has "G" in mutated_transcript, then the total number of A_to_G for that position is 20. Likewise I would like to calculate total number of base "A"s is mutated to "G"s (and vice versa) in all reads at every possible position and sum it up so that I get count for total number of base A mutated to G for the entire transcript.

    Kindly guide me

    Thanks in advance

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