Do you mean the GenCode reference _/annotation/_ gtf dataset? This is
not a reference genome. If you want to use a _/custom reference
genome/_, this would be provided as a fasta file, using these
My guess is that you have done the following (since a gtf file would not
be accepted as a custom reference genome unless you changed the datatype
to be "fasta"):
-> provided the GenCode gtf file as a "reference annotation" dataset and
for mapping used a built-in "reference genome" or mapped somewhere else.
When there are issues, it is most often a reference genome chromosome
identifier mismatch problem. This wiki section explains this issue in
Sometimes this issue can be corrected by altering the identifiers in the
gtf file to match those in the reference genome (what your fastq data
was mapped to, convert BAM->SAM to see the identifiers if necessary).
This FAQ shows one method:
Hopefully the resources here help to resolve the issue!
ps. This did not post to the mailing list because the "to" was not to
just the mailing list. Please post new questions that way, or much
better (since this mailing list will be retired very soon), please
activate your account at Galaxy Biostar and post your question there
(this has replaced the galaxy-user mailing list). Here is how:
On 5/20/14 12:55 AM, Mark Lindsay wrote:
when I run Cuffmerge using the latest GenCode v19 GTF as a reference
genome….this fails to run…tried this using multiple approaches and datasets.
Of note…...Cuffmerge works fine when the Gencode GTF is omitted as a reference
genome. CuffCompare also works fine when the same Gencode GTF is used as a
Presumably there is something wrong with the Cuffmerge set-up relating to the
reference genome? Or am I doing something wrong.
The Galaxy User List is being replaced by the Galaxy Biostar
User Support Forum at https://biostar.usegalaxy.org/
Posts to this list will be disabled in May 2014. In the
meantime, you are encouraged to post all new questions to
For discussion of local Galaxy instances and the Galaxy
source code, please use the Galaxy Development list:
To manage your subscriptions to this and other Galaxy lists,
please use the interface at:
To search Galaxy mailing lists use the unified search at: