Post date: Oct 14, 2015 10:13:38 PM
There was a mistake in the script I used to infer sequence-based Fst for the ecotype pairs with v0.3 LG information. It used the wrong locus id file. I have fixed this. In /labs/evolution/projects/timema_speciation/timema_radiation/popgen/popgen/ correct estimates of Fst are in nei20kSan_tcrist_HV (or MR1, R12 and L). Likewise, lgSorted20kbsSanityTcr.txt gives LG and scaffold ids in order for these 20kb windows based on v02. A different file, sortedLgV02toV03.txt, gives the same information but for v03 (NAs for those not on a v03 LG). An R script fstPlotsTcr.R makes Fst plots based on both orderings for these 20kb windows. Finally, fstTcristV03.txt contains the Fst estimates for all four ecotype pairs in v03 order.