Anyone using BFDstar and trying to get their SNP alignment in binary format?
They have a pretty good tutorial, but I am having trouble using the R package phrynomics to convert my data.
I keep getting this message:
> TranslateBases(snpdata, translateMissing = FALSE, ordered = FALSE)
Error in `[
For BFD* (Beast and SNAPP) you only need your SNPs in Nexus format, which Beauti can load and convert to XML. I haven't used the phrynomics R package, so I can't help you there.
Also, make sure you go get the most recent version of the BFD tutorial off of Adam Leache's website, as there is new information on the specification of priors that is missing from earlier versions. Additionally you will want to read the "Rough guide to SNAPP" for more information on understanding the parameters that you are setting in Beauti.
What format is your data currently in?
My data is in nexus, however they say on the BFD tutorial the input needs to be in binary format. That is my struggle.
No, it can be in standard [ACGT] format, but SNAPP does assume SNPs to be unlinked and biallelic. Just load the Nexus alignment in Beauti and then work on specifying appropriate priors. The default priors will not work properly.
Also I forgot to mention that it can be a little finicky about what version of Java (7 vs 8, proprietary vs open-source) and Beast that you are running (in my experience), and as well the exact format of the XML has changed with different versions of SNAPP, so make sure that you have the most recent version of the tutorial (which is actually dated 2017). If you have any issues feel free to message me- it took me a long time to get it working properly.
Thank you so much! Some of these are very tricky indeed.
I will message you if I need!
Hi Silvia,
I know this post/thread is from last year. But did you ever get this figured out and get the BDF* approach to work for you? I have used the Leache and Ogilvie tutorial as well with no issues, and subsequently published using the method. Although their tutorial is really good, in the spirit of open science, I just published a public Gist ("Method for Analyzing ddRADseq Data in SNAPP (BEASTv2.4++)": https://gist.github.com/justincbagley/8f1a263790609ed5275db065aa96b42b) containing a basic series of steps (including basic NEXUS format and phyrnomics) for analyzing ddRAD-seq data in SNAPP. These are just the steps that I used. People can email me for more details, and perhaps encourage me to add them to the Gist; but maybe this could be useful to you or to someone else who finds this thread. Best, ~J
Thank you Justin!
I figured out what I was doing wrong... But I will look you Gist up!
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