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MartaPelizzola / ACER

Adapted chi-squared and CMH test to evolve and resequenced data. Includes drift and pool sequencing variance in the tests
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Using ACER from SYNC files #1

Open orijitghosh opened 5 years ago

orijitghosh commented 5 years ago

Hi, I will love to use this tool for my analysis, till now I have been using Popoolation2. So I have sync files for my populations. I wanted to know the frequency table of alleles, is it a SYNC file or some other format? It will be really helpful to me if you can give me a detailed example of how to run ACER. Sorry for being naive in this regard. Thanks in advance

MartaPelizzola commented 5 years ago

Hi, I answered your email. Sorry for overlooking the issue here. Let me know if you did not receive it.

Calebhubb commented 3 years ago

Hi Marta: I actually had a similar question. I am also using Popoolation 2, and was curious as to what file format this program requires to input into it. Thanks! Caleb

MartaPelizzola commented 3 years ago

Hi Caleb, Thank you for your interest and question. The file format for our program is a matrix of allele frequencies and a matrix of coverages. The rows of the matrix are the SNPs. Depending on which function you are using columns might be time points and/or pools from one or more replicates. From a SYNC file, for each SNP and each sample you need to extract the count of the allele of interest divided by the coverage for the allele frequency matrix, and the coverage value for the coverage matrix. You can also use the package https://github.com/popgenvienna/poolSeq to extract the relevant information from SYNC files.

Let me know if you have other questions. All the best, Marta