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  • RNA-seq alignment to closely related genome

    Hi,

    I have recently done alignment of an RNA-seq library for an organism (bos indicus cattle, the zebu cattle) without reference genome to a closely related genome (bos taurus cattle). The mapped percentage looked OK.

    I have little idea how similar these two genomes are, probably over 99.9%.

    I am a bit concerned about some sort of bias introduced due to the use of a 'different' reference genome, particularly for less conserved genes. Is there any way I can look at this bias formally? I have thought about de novo assembly, but that's probably not practical given the low depth (one lane, about 20M 75bp paired end reads) and insufficient computing power (16G RAM).

    Any thought is welcomed.

    Thank you!

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