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, doanea(a)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
=====================================================================
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.
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at
usegalaxy.org. Please keep all replies on the list by
using "reply all" in your mail client. For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:
http://lists.bx.psu.edu/listinfo/galaxy-dev
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
--
Jennifer Hillman-Jackson
http://galaxyproject.org