Hello Ashley,

There could be a genome mismatch problem, this part of support wiki covers how to check:
https://wiki.galaxyproject.org/Support#Reference_genomes

The good news is that if a different version of the human assembly was used, a custom reference genome can be used with Trackster. In general you would want to avoid that with larger genomes, but it can be better than re-running analysis in some cases (you just want to visualize). The basic idea is to load the fasta version of the genome you did use into your history and build a visualization from there.
https://wiki.galaxyproject.org/Support#Custom_reference_genome

To my knowledge there are no known issues with Trackster, but if more is found out (now, after the holiday), we will send an update.

Best,

Jen
Galaxy team

On 12/27/13 4:31 AM, doa...@mskcc.org wrote:
Hello,

I've been using Galaxy for RNA-seq analysis. Many thanks for this great resource!

I have run into a problem that I hope someone might be able to help me with. When loading my .BAM files and/or .gtf files into trackster, I get an error stating: "Input error: Chromosome chrDecoy found in your input file but not in your genome file."

My Illumina fastq files were QCed and aligned using tophat to hg19, and I used cufflinks with hg19 as annotation guide. All my files have hg19 as the dbkey.

My guess is that the hg19 I used as a reference differs form the built in model, but I am not sure how I might fix this. Fwiw, I am able to load all my data into IGV, using hg19 as the genome, and visualize everything.

Any suggestions would be really appreciated!
Thanks!

Ashley

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