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