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Hi all,
I have assembled a de novo transcriptome for my organism of interest (in this case, the eastern oyster). The genome of a related species was recently released (pacific oyster). I have aligned my representative transcripts to the genome of the related species. I would now like to calculate dn/ds between the two species for each of the aligned transcripts. Right now, the only idea I have for how to do this is to take each individual transcript, realign it with the appropriate scaffold from the related genome, and analyze it with DnaSP or PAML.
Does anyone know of a way to take the full alignment in SAM or BAM and calculate dn/ds either for the entire genome or for each exon/transcript?
Thanks for your thoughts!
Laura
I have assembled a de novo transcriptome for my organism of interest (in this case, the eastern oyster). The genome of a related species was recently released (pacific oyster). I have aligned my representative transcripts to the genome of the related species. I would now like to calculate dn/ds between the two species for each of the aligned transcripts. Right now, the only idea I have for how to do this is to take each individual transcript, realign it with the appropriate scaffold from the related genome, and analyze it with DnaSP or PAML.
Does anyone know of a way to take the full alignment in SAM or BAM and calculate dn/ds either for the entire genome or for each exon/transcript?
Thanks for your thoughts!
Laura
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