How to prepare aFCs

[okendojo]

Could you share the procedure on how to prepare aFCs? The link you provided is nolonger woking

[navaehsan]

Thanks for your message. I updated the link and it should be working now. Please let me know if you I can provide more information.

[okendojo]

It is now working on a project where I have two sets of F0 (grand parents) in A, B, C, and D. A was crossed with B ( AxB) and C was crossed with D ( C x D) to give us the F1 generation AB and CD. The female AB was then crossed with the male CD to give us the F2 generation have ABCD haplotypes. We have the illumina DNA sequence from the four grand parents (A, B, C, and D). We also have the RNAseq, from F2 (ABCD). I wanted to use your approach to do haplotype specific gene expression considering the fact the the F2 is a mixed of four different haplotypes from F0. Do you have an idea on how I can go about this? Do let me know.

[navaehsan]

This work is based on the information of eQTL data and the prediction method uses the allelic Fold Change (aFC) information of the eQTL SNPs. If you have that data for your project then this method would help.