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Hi everyone,
I'm currently analyzing some sequencing data in my lab, and one of the things we intended to do was to map the reads from a bunch of offspring to 2 parental lines. In other words, we are trying to determine which genomic regions came from each parent.
Our methods involved the use of a program called MSG, which automates the whole process of mapping to both parents and determining from which line specific genomic regions come from. The issue we just ran into is that MSG requires the reads to be produced using restriction enzymes. Unfortunately for us, we used the Illumina Nextera DNA Prep Kit, which relies on the use of transposomes to fragment and add adapters to the DNA ("tagmentation").
Has anyone ran into an issue like this before, or has anyone used any other software to map to two parental strains?
Thanks a lot for the help!
I'm currently analyzing some sequencing data in my lab, and one of the things we intended to do was to map the reads from a bunch of offspring to 2 parental lines. In other words, we are trying to determine which genomic regions came from each parent.
Our methods involved the use of a program called MSG, which automates the whole process of mapping to both parents and determining from which line specific genomic regions come from. The issue we just ran into is that MSG requires the reads to be produced using restriction enzymes. Unfortunately for us, we used the Illumina Nextera DNA Prep Kit, which relies on the use of transposomes to fragment and add adapters to the DNA ("tagmentation").
Has anyone ran into an issue like this before, or has anyone used any other software to map to two parental strains?
Thanks a lot for the help!