I want to work on wheat genomics, for doing this I am not sure where to get the reference sequence for wheat because if you go to ensembl at this link wheat genome then there comes many things to download. Same happens for NCBI. I have downloaded a reference sequence from ensembl but that sequence is not showing the chromosome number and can I use that for my further analysis?
The latest wheat genome consists of a number of scaffolds. Where it is known which chromosome the scaffold belongs to, they contain the chromosome in the scaffold name, for example the scaffold TGACv1_scaffold_250239_3DL is part of chromosome 3DL. There is more information about the assembly here: http://plants.ensembl.org/Triticum_aestivum/Info/Annotation/