Bulk Segregant Analysis using next generation sequencing data

Question

[p.weru]

I am relatively new to bioinformatics and especially in working with next generation sequencing data. I am working on a study that aims to identify polymorphisms that are associated with a certain phenotype. I intend to do this through bulk segregant analysis where I have whole genome sequences of two bulks, each comprising 10 individuals. The aim is to determine allele frequencies in order to try and determine any association with the phenotype. I am not sure how to proceed! Can someone kindly advise me on how this is done and which software I can use (preferably one that is not command line based). I have been using CLC Workbench but it seems like it has limitations in conducting this type of analysis. Any help will be greatly appreciated.

Kind regards,
Peterson

Answer 1

[marina.v.yurieva]

If you don't want to use command line than you are probably better off with CLC. It shows allele frequency and can do the analysis in bulk. I'm not sure what is it you are trying to do that CLC doesn't do. You can also try Galaxy.

[p.weru]

Thanks a lot. I have used GALAXY before for variant detection and so I will explore it further to see how analysis on allele frequency can be done. I will also explore CLC further as it seems I am not familiar with functionality for conducting this kind of analysis. Thanks.

Answer 2

[matted]

This recent review has some pointers to tools in this field: "Sequencing pools of individuals - mining genome-wide polymorphism data without big funding" (Nature Reviews Genetics, 2014). I would recommend that you become comfortable with the command line and statistical computing environments like R, since most advanced methods in this field aren't GUI-based.

[p.weru]

Thanks very much. I agree that lacking skills in command line is real handicap in bioinformatics. I am slowly trying to learn the ropes. The review provides some very useful information that will give me more insights. Cheers.

Answer 3

[cremeglace]

If you are comfortable with basic command line and Python, this tutorial might be useful.