We had downloaded the custom build O_sativa from MSU version7 as our reference genome for Tophat alignment. We get this message.
The errors from IGV after the Tophat alignments are as follows:
" File: C:\Users\sqiu\Desktop\Julie\Galaxy104-[Tophat_for_Illumina_on_data_83,_data_82,_and_data_100__accepted_hits].bam
does not contain any sequence names which match the current genome.
File: ChrSy.fgenesh.gene.1, ChrSy.fgenesh.gene.10, ChrSy.fgenesh.gene.11, ChrSy.fgenesh.gene.12, ...
Genome: Chr1, Chr2, Chr3, Chr4, ... "
Can you please suggest how to solve this problem?