Chris, The problem is likely a bug in the Cufflinks wrapper that was recently fixed in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/ff7c8c0bef60 Try updating your Galaxy instance to include this changeset; if this doesn't fix the problem, let us know. Good luck, J. On Nov 11, 2011, at 10:44 AM, Bidwell, Christopher A. wrote:
Colleagues,
We have set up a local Galaxy but I am having trouble running Cufflinks with the annotation gtf file. We have the iGenomes btau4.2 genome in the database and use the iGenomes btau4.2 gtf file in the history. However the –G isn’t showing up in the command line (below) and the output is the same as when I run cufflinks without annotation.
Is something not set up correctly?
Info: cufflinks v1.0.3
cufflinks -q --no-update-check -I 50000 -F 0.050000 -j 0.050000 -p 4 -N -b /phillip/hiscansq/run00085-09-16-11_D0D1KACXX/110916_H179_0062_AD0D1KACXX/hr00206_OAR13-24/References/Bos_taurus/genome.fa
The details page shows the gtf file being supplied from the history
Input Parameter Value SAM or BAM file of aligned RNA-Seq reads 26: Tophat for Illumina on data 2 and data 1: accepted_hits Max Intron Length 50000 Min Isoform Fraction 0.05 Pre MRNA Fraction 0.05 Perform quartile normalization Yes Conditional (reference_annotation) 1 Reference Aonnotation 24: Btau42_iGenomes_annot.gtf Conditional (bias_correction) 0 Conditional (seq_source) 0 Conditional (singlePaired) 0
Thanks for your help. Chris ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: