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 more detail: https://wiki.galaxyproject.org/Support#Reference_genomes.
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: https://wiki.galaxyproject.org/Support#Biostar
On 5/20/14 12:55 AM, Mark Lindsay
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 reference genome.
Presumably there is something wrong with the Cuffmerge set-up relating to the reference genome? Or am I doing something wrong.