I am very new to genomics and have been given scripts from other bioinformaticians to learn from. Within these scripts they used specific .bed files to analyse a panel of genes and perform annotation.
I understand there are methods of turning a .fasta file or a .bam file into a .bed file. However, I do not understand how to extract information from specific genes e.g. how to create a .bed file which maps all the collagen genes or how to create a .bed file with only exons.
Does anyone know the process of performing such analysis, or know of any databases where .bed files may be stored?
Many thanks, Krutik