Hello Tim,
The problem is either that the reference genome build used does not
contain the mitochondrial genome sequence, that the reference annotation
file that you are using with the Cufflinks does not include
mitochondrial annotation, or that the identifiers between the reference
genome and the reference annotation are a mismatch (one is labeled "M"
and the other "chrM" or possibly "MT").
Some links to the build:
http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/mouse/
http://www.ncbi.nlm.nih.gov/genome?term=mus%20musculus
(open "Representative" to see the Mito as "MT", it is not listed
on either link under chromosomes.)
If you pulled out the fasta sequence yourself and are using it as a
custom reference genome on the public Main Galaxy instance at
https://main.g2.bx.psu.edu/ (usegalaxy.org) or installed it locally,
then it could be missing the mito chromosome/genome.
If you are using another public or private/local Galaxy (not Galaxy
Main), you can contact them to find out how the genome was created (if
it included the mito).
For either of the two above - you could also run a tool like "NGS:
Picard (beta -> BAM Index Statistics" to see if the mito chromosome is
present in the Tophat output and what it is named. If included, compare
the chromosome identifier/name to the reference annotation file your are
using. The identifiers must be exact or tools will not function
properly. More help, please see:
http://wiki.galaxyproject.org/Support#Tools_on_the_Main_server
An alternative is to use either the mm9 or mm10 genome at the public
Galaxy Main Galaxy instance. The variants, described on the "NGS:
Mapping -> Bowtie" tool form, contain the mito chromosome named as
"chrM". These are sourced from UCSC:
http://genome.ucsc.edu/goldenPath/credits.html#mouse_credits
also navigate to "Genomes -> mammal -> mouse -> mm10" to see more details
Hopefully this helps,
Jen
Galaxy team
On 2/19/13 9:43 AM, Brown, Tim wrote:
I have RNA-seq data that I have run through Tophat using the mouse mm10
grc38 reference genome. When I use Cufflinks on these data, the
mitochondrial genome transcripts are excluded from the analysis. I
would like to see that data. Is there an option within the toolbox that
can remedy this? I'm a newb here.
Thanks for any help,
Tim
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___________________________________________________________
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,
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