Question: Chrdecoy Error In Trackster
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4.9 years ago by
doanea@mskcc.org10 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 ===================================================================== Please note that this e-mail and any files transmitted from Memorial Sloan-Kettering Cancer Center may be privileged, confidential, and protected from disclosure under applicable law. If the reader of this message is not the intended recipient, or an employee or agent responsible for delivering this message to the intended recipient, you are hereby notified that any reading, dissemination, distribution, copying, or other use of this communication or any of its attachments is strictly prohibited. If you have received this communication in error, please notify the sender immediately by replying to this message and deleting this message, any attachments, and all copies and backups from your computer.
rna-seq cufflinks • 921 views
ADD COMMENTlink modified 4.9 years ago by Jennifer Hillman Jackson25k • written 4.9 years ago by doanea@mskcc.org10
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4.9 years ago by
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Jennifer Hillman Jackson25k wrote:
Hello Ashley, 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. Best, Jen Galaxy team -- Jennifer Hillman-Jackson
ADD COMMENTlink written 4.9 years ago by Jennifer Hillman Jackson25k
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