your pid must also be empty.

I think:

-s <seq_dir> Causes cuffcompare to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that <seq_dir> must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.

might help

--- On Thu, 7/14/11, Richard Mark White <whiter3@yahoo.com> wrote:

From: Richard Mark White <whiter3@yahoo.com>
Subject: [galaxy-user] rna-seq CDS, splicing and TSS fails
To: galaxy-user@lists.bx.psu.edu
Date: Thursday, July 14, 2011, 7:53 AM

Hi all,

So I am using cuffdiff to find significant differences between two samples (no replicates). The transcript and gene differential expression works and I get significant values. However, consistently, the TSS, CDS, and splicing differences return with "1 line" and no data. I have tried multiple different GTF transcriptome reference files - UCSC refflat, ensembl, but still no luck.

Maybe I am missing something very basic - can anyone give me advice here?

Richard

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