Question: reference genome error
0
gravatar for qiushuhao1985
3.9 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 3.9 years ago by Jennifer Hillman Jackson25k • written 3.9 years ago by qiushuhao198510
0
gravatar for Jennifer Hillman Jackson
3.9 years ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

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 http://usegalaxy.org, but the general strategy will be the same for any genome comparison:
http://wiki.galaxyproject.org/Support#Reference_genomes

Best, Jen, Galaxy team

ADD COMMENTlink written 3.9 years ago by Jennifer Hillman Jackson25k
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