Hi, As a first guess I would say that your chromosome names do not match somewhere along the line. If you look at your sam file and the fasta of the genome you are working with (and the gtf file as well if you are using it) you may find, for example, one refers to chromosome 1 as "chr1" whilst the other refers to chromosome 1 as "1" or even "Chr1" or some other way of referring to the chromosome - any of these mismatches can cause you to get an empty output. If you are using a built in index it may be you need to change your chromosome names from "1" to "chr1" for example. Amazingly, the names of human chromosomes are apparently not yet standardised across all databases for the human genome (and I presume this may be the case for other genomes as well). Best Wishes, David. __________________________________ Dr David A. Matthews Senior Lecturer in Virology Room E49 Department of Cellular and Molecular Medicine, School of Medical Sciences University Walk, University of Bristol Bristol. BS8 1TD U.K. Tel. +44 117 3312058 Fax. +44 117 3312091 D.A.Matthews@bristol.ac.uk On 15 Jun 2011, at 02:22, Michael Gooch wrote:

I attempted to run cufflinks on some RNA sequencing data. It seemed to complete without any errors, but the output files were empty. I am trying to figure out if I did something wrong or whether my data needs some additional processing before cufflinks will be able to use it. (Or whether the data is unsuitable for cufflinks.) The data is paired end reads.

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