Dear Dr. Hiller,
Thank you for making your valuable tools and datasets publicly available. I am currently working on genotype–phenotype association mapping in plants (referred to as cross-species GWAS by my supervisor), and I have found your tools particularly relevant and promising for my research.
As I followed the step-by-step usage of your published data on vision loss (https://bds.mpi-cbg.de/hillerlab/ForwardGenomics/loss_of_vision/), I encountered a few issues that I have not been able to resolve, and I would greatly appreciate your guidance:
1. I noticed that in some GitHub issues, other researchers mention using mafIndex and mafExtractor to preprocess the MAF files. However, I couldn’t find any mention of these tools or preprocessing steps in the README or in the methods sections of your publications. Could you kindly clarify whether these steps are required and, if so, where I might find the relevant documentation?
2. I’m currently aligning multiple plant genomes using Cactus, which outputs HAL files. I would like to use the resulting MAF files (converted from HAL) for analysis with ForwardGenomics. However, I noticed some differences between these converted MAFs and the MAFs you provided in the vision loss dataset. Would ForwardGenomics still be applicable in this case? Are there additional formatting or filtering steps needed?
I’m still at the early stage of working in comparative genomics, so I apologize if my questions are somewhat basic. Any advice, clarification, or experience you could share would be greatly appreciated.
Thank you very much for your time and for developing these important resources.
Best regards,
Jingchen Yuan
PhD student, Institute of Genetics and Developmental Biology (IGDB)
Chinese Academy of Sciences (CAS)
Dear Dr. Hiller,
Thank you for making your valuable tools and datasets publicly available. I am currently working on genotype–phenotype association mapping in plants (referred to as cross-species GWAS by my supervisor), and I have found your tools particularly relevant and promising for my research.
As I followed the step-by-step usage of your published data on vision loss (https://bds.mpi-cbg.de/hillerlab/ForwardGenomics/loss_of_vision/), I encountered a few issues that I have not been able to resolve, and I would greatly appreciate your guidance:
1. I noticed that in some GitHub issues, other researchers mention using mafIndex and mafExtractor to preprocess the MAF files. However, I couldn’t find any mention of these tools or preprocessing steps in the README or in the methods sections of your publications. Could you kindly clarify whether these steps are required and, if so, where I might find the relevant documentation?
2. I’m currently aligning multiple plant genomes using Cactus, which outputs HAL files. I would like to use the resulting MAF files (converted from HAL) for analysis with ForwardGenomics. However, I noticed some differences between these converted MAFs and the MAFs you provided in the vision loss dataset. Would ForwardGenomics still be applicable in this case? Are there additional formatting or filtering steps needed?
I’m still at the early stage of working in comparative genomics, so I apologize if my questions are somewhat basic. Any advice, clarification, or experience you could share would be greatly appreciated.
Thank you very much for your time and for developing these important resources.
Best regards,
Jingchen Yuan
PhD student, Institute of Genetics and Developmental Biology (IGDB)
Chinese Academy of Sciences (CAS)