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Hello everyone,
We have embarked on a wonderful journey into the world of selective sequencing using ddRAD-Seq. We are specifically mapping recombinant (hopefully) progeny back to the parents to assess what parent contributed which DNA in each progeny. This has been done using bowtie2 and samtools. Following which we have used STACKS (http://catchenlab.life.illinois.edu/stacks/) to generate progeny maps using sequenced reads from the two parental genotypes. However, this has produced a large genotype matrix riddled with holes (see attached).
Since both parents are sequenced, I assume there's a better way to do this so that we can use all of the data from each sequenced progeny without relying on those same loci to be sequenced in the parents. There's a review from Mark Blaxter's lab in 2011 (https://web.natur.cuni.cz/~muncling/NGS2.pdf) that alludes to a statistical method of calling parental contributions using SNPs frequencies but I have yet to see this implemented anywhere. Is there a program that is able to do this given two parental genotypes and the raw or mapped reads?
Thank you
Matt
We have embarked on a wonderful journey into the world of selective sequencing using ddRAD-Seq. We are specifically mapping recombinant (hopefully) progeny back to the parents to assess what parent contributed which DNA in each progeny. This has been done using bowtie2 and samtools. Following which we have used STACKS (http://catchenlab.life.illinois.edu/stacks/) to generate progeny maps using sequenced reads from the two parental genotypes. However, this has produced a large genotype matrix riddled with holes (see attached).
Since both parents are sequenced, I assume there's a better way to do this so that we can use all of the data from each sequenced progeny without relying on those same loci to be sequenced in the parents. There's a review from Mark Blaxter's lab in 2011 (https://web.natur.cuni.cz/~muncling/NGS2.pdf) that alludes to a statistical method of calling parental contributions using SNPs frequencies but I have yet to see this implemented anywhere. Is there a program that is able to do this given two parental genotypes and the raw or mapped reads?
Thank you
Matt