There could be a genome mismatch problem, this part of support wiki
covers how to check:
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.
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.
On 12/27/13 4:31 AM, doanea(a)mskcc.org wrote:
I've been using Galaxy for RNA-seq analysis. Many thanks for this
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
Any suggestions would be really appreciated!
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