Hi all,
I've been having trouble running my Arabidopsis thaliana NGS pipeline in 
galaxy. Specifically, tophat alignment to the built-in-index worked fine 
(visual assessment in IGV) but I couldn't get cufflinks/Cuffduiff to run using 
the same annotation.gtf file I'd used in the alignment. Error message = Error 
running cufflinks. return code = -11 cufflinks: /lib64/libz.so.1.
Cufflinks/cuffdiff would run without the annotation file and give a 
differential expression output but without the annotation file the gene_id was 
meaningless (XLOC_000001 etc) and all I had was a locus for a region with 
differential expression.
After a lot of frustration I re ran the alignment using a custom built genome 
and annotation file from Illumina: http://cufflinks.cbcb.umd.edu/igenomes.html  
and hey presto, cufflinks/cuffdiff work fine. I did try altering using both 
chr1 and 1 for chromosome name as a discord between the chromosome naming 
seemed to frequently be a problem. Apart from this, what other reasons could 
there be for the built-in-index not working with annotation.gtf files? Is this 
an issue with the built-in-index (Mouse-ear Cress (Arabidopsis thaliana): 
Tom SmithUniversity of York, UK                                           
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