Hi Jen,

Thanks for the reply.  I am using the Galaxy Main instance, and simply
chose the mm10 reference genome from the pull-down option list.  The BAM
index statistics on one of my Tophat files reports that it has a large
number of reads that are aligned to to chrMÅ  so at least the alignments
are there.  I used the same mm10 reference genome with Cufflinks.  Since I
didn't use a custom genome, it seems as though there should not be any
identifier mismatchesÅ (?)

Tim






On 2/19/13 1:54 PM, "Jennifer Jackson" <j...@bx.psu.edu> wrote:

>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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>
>-- 
>Jennifer Hillman-Jackson
>Galaxy Support and Training
>http://galaxyproject.org


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