Hello Mark,
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
instructions: https://wiki.galaxyproject.org/Support#Custom_reference_genome
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.
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:
https://wiki.galaxyproject.org/Support#Tools_on_the_Main_server:_RNA-seq
-> https://usegalaxy.org/u/jeremy/p/transcriptome-analysis-faq#faq5
Hopefully the resources here help to resolve the issue!
Best,
Jen
Galaxy team
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
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https://wiki.galaxyproject.org/Support#Biostar
On 5/20/14 12:55 AM, Mark Lindsay wrote:
Dear All
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.
Best wishes
Mark
--
Jennifer Hillman-Jackson
http://galaxyproject.org
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