Question: reference genome error
gravatar for qiushuhao1985
3.7 years ago by
United States
qiushuhao198510 wrote:

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? 

Thank you!

ADD COMMENTlink modified 3.7 years ago by Jennifer Hillman Jackson25k • written 3.7 years ago by qiushuhao198510
gravatar for Jennifer Hillman Jackson
3.7 years ago by
United States
Jennifer Hillman Jackson25k wrote:


This looks like a reference genome mismatch problem. You will need to check the version of the genome used for mapping against the genome hosted at a public site (Galaxy, IGV, any).

These instructions are targeting at aiding users to compare data to that hosted on the public Galaxy instance at, but the general strategy will be the same for any genome comparison:

Best, Jen, Galaxy team

ADD COMMENTlink written 3.7 years ago by Jennifer Hillman Jackson25k
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