Cuffdiff 0 tests with iGenomes?...

[hbt]

I'm trying to run a number of data sets with the most recent version of cuffdiff.

Previously with Cufflinks 2.02 I would provide cuffdiff with the .Bam files from tophat2 (2.04) and both the genome.fa file (for bias correction) and .gtf annotation from the iGenomes package.

However this now results in cuffdiff producing 0 tests in its differential analysis step. The software seems to otherwise run to completion without throwing an error.
e.g....

"Processed 20972 loci.
Performed 0 isoform-level transcription difference tests
Performed 0 tss-level transcription difference tests
Performed 0 gene-level transcription difference tests
Performed 0 CDS-level transcription difference tests
Performed 0 splicing tests
Performed 0 promoter preference tests"

I know the convention is to run the .bam files through cufflinks then cuffcompare/cuffmerge to produce a combined annotation .gtf but going straight to cuffdiff with the .bam files has always worked well for me in the past (and saves some time).


Has anyone else come accross this issue and is it a problem with the most recent versions of iGenomes or cufflinks?


many thanks

Huw

[TiborNagy]

I think this will be a trivial error. Please check your BAM files. How many mapped reads do you have? Try to systematically check the input and output files in each step.