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): Arabidopsis_thaliana_TAIR10)? Cheers, Tom SmithUniversity of York, UK