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I have bulk RNAseq data from two strains of mice from Jackson Lab: C57BL/6 and B6.SJL.

The former expresses a Ptprc-b allele and the latter expresses a Ptprc-a allele.

They are supposedly isogenic at all other loci. But to the best of my knowledge, there is no empirical evidence of this.

My question is, how would I go about finding all the homozygous single nucleotide variations (if there are any) in the coding sequences of the two strains from my RNAseq data.

I should mention that the RNAseq data are paired-end illumina reads ~150bp long.

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  • $\begingroup$ Maybe try MMseq or MMseqs2? $\endgroup$
    – M__
    Commented Jul 6, 2023 at 22:58

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