Here is a phylogenetic network of wild annuals. This is made from GBS data, aligned against the celera assembly. This is ~40,000 sites which have 2 alleles and <20% missing data.
Here is a excel file that describes the samples: GB_GBSdesign
The JPEG looks horrible, download it as a pdf: 213i_80m
Tab delimited under the fold:
I’ve done a small analysis on my GBS data and posted it on my blog: http://www.proseedwithscience.com/?p=816
Edit: This is mostly just a quick look at the amount of missing data in the data and some potential explanations of where it might be from.
Some SNP table to useful table conversion scripts are here: FormattingScripts_v0.4
Readme.txt explains usage, makes fasta, bayescan, structure files as well as converting to digits for R.
Let me know if you find any of this useful or broken.
Greg
Edit: updated small fix to structure formatter
I’ve just noticed there is a problem with code that has been dropped into posts. If you copy and paste directly from the post, for some reason, depending on the syntax of the code you may lose important bits. For example “while ()” appears as “while ()” but thats not what it is! Click on edit and see for yourself! You will not have this problem if you go to the edit post page and copy from there. Also and this may just be the text editor I use but some commented line were broken into multiple lines which did not have ‘#’.
There has to be a better way to host code here but I don’t know what it is. Any ideas?
Rose coded this up as a faster and efficient way to combine all the snp calls into one table. I’ve made a few modifications, hopefully its not broken. Updates are likely in the future.
Email for v7. Bug found that printed G’s as C’s and vise versa.
Call SNPs from sam files in a method similar to Hohenlohe et al 2010. Updated to v4 Feb 9. Previous version had a bug.
It is now fixed up for all of BWAs cigars flavors.
This only deals with reads that fit one of the following:
Full alignment (55M)
Soft clip at the start (10S45M)
Soft clip at end (45M10S)
One deletion (25M10D25M)
One insertion (20M10I20M)
This means it ignores reads with a cigar fields that have N, H, P, = or X and it ignores reads with a cigar more complicate then a single soft clip or a single indel. It also does not penalize reads adjacent to indels.
It ignores bases in soft clipped parts of reads
Ask me for the most current version if you want to use any of these!
A few perl scripts that take a SNP table and do the following:
1. Remove unwanted samples and rename the samples
2. Remove sites that do not have enough data
3. Order the sites based on a map
Ask me for the most current version of these if you want to use them.
Several people in the lab are now working with very similar data (in structure) and have similar questions (in technique). As I have discussed with several people it would be very useful if we could all build up and share the tools needed to do these analysis. Understandably, people may want to do things on their own or in a specific manner, but I think there are several advantages to building this up together. The main thing is that it will be more efficient in terms of personnel time, having each person re-invent the wheel does not make sense. I think the blog is a great place to set do this. Below we can make our wish list and link to posts for solutions as they become available. As always, the principles (1,2 and 3) covered here apply.
Here are the transcriptome assemblies ordered based on the map Chris made. The columns are contig name, Linkage group, and CentiMorgan.
The Trinity Assembly ordered
The 16000 gene assembly
Greg B.
This is a useful tool for anyone who uses ssh. It allows you to close your terminal and still have processes running. This is very useful if you are using a laptop for example. You can check in on the process from anywhere afterwards.