Karen's Lab Notebook

I was interested in identifying putative AxB F1 hybrids in the 2018 D8 individuals. First I took all A and B individuals from D8, regardless of year. I then found all SNPs that were fixed reference in A and fixed alternate in B, or vice versa. I next pulled out all the 2018 D8 individuals and called those same SNPs, and polarized the genotypes as B (dos0), A (dos2), or heterozygous. Not surprisingly, all 7 D8 2018 A individuals were 100% A. Another 8 individuals had a prop het between 0 and 0.9. These could be recombinant hybrids between A and B, or something else. March20_2018_D8_16 and March20_2018_D8_33 look a bit like backcrosses for example. March20_2018_D8_37 could be a F1 hybrid with high error rates in calling heterozygotes. Another 43 individuals look like they could be F1 hybrids between A and B. They are over 90% heterozygous for SNPs fixed between A and B. This is more F1 hybrids than you had on your piecharts Alan, why the discrepancy?  I was worried about al...

Trying to decide how to deal with mapping the more distant species. Specifically Obtusa and Simocephalus. A couple of different considerations. 1) Obtusa is not that divergent from Pulex. Simocephalus is VERY divergent. So maybe divergent mapping and using a different mapper is more of a concern for Simocephalus than Obtusa. 2) What are we using the outgroups for? Why do we want to map them? For Obtusa, which is less divergent, we have two reasons. 1) We want to use them as an outgroup to polarize SNPs in the Pulex dataset. 2) We want to construct a pseudoreference genome for Obstusa to use for competitive mapping with pooled data. Where I am right now: I looked at the input fastq file size, the final bam file size, and the number of reads mapped in that final bam (using samtools flagstat), and compared 12 Obtusa samples and 16 Pulex samples from the same plate of libraries. As you can see in the graph below, there is a positive correlation between incoming fastq ...