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 <[email protected]> wrote:
From: Richard Mark White <[email protected]>
Subject: [galaxy-user] rna-seq CDS, splicing and TSS fails
To: [email protected]
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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