Hi,

I am running paired alignments with tophat and when I run cufflinks

./cufflinks -o emrsa15.cuff/ -g annotation.gtf accepted_hits.bam

cufflinks doesn't process the loci, so all the output files are empty (only header is appeared)

Cufflinks output

 Inspecting reads and determining fragment length distribution.
> Processed 1 loci.                            [*************************] 100%
> Map Properties:
>       Normalized Map Mass: 19021202.87
>       Raw Map Mass: 19021202.87
>       Fragment Length Distribution: Empirical (learned)
>                     Estimated Mean: 213.28
>                  Estimated Std Dev: 91.26

Here is the summary of the alignment, which seems fine.

Left reads:
          Input     :  18922184
           Mapped   :  18759527 (99.1% of input)
            of these:     41369 ( 0.2%) have multiple alignments (1463 have >20)
Right reads:
          Input     :  18922184
           Mapped   :  18494767 (97.7% of input)
            of these:     41039 ( 0.2%) have multiple alignments (1463 have >20)
98.4% overall read mapping rate.

Aligned pairs:  18412669
     of these:     40472 ( 0.2%) have multiple alignments
                  143680 ( 0.8%) are discordant alignments
96.5% concordant pair alignment rate.

When I run tophat with one end, cufflinks works fine. But not with the paired ends.

Do you have any suggestion why is that happening or how can I merge the results of cufflinks from the two ends?

I would appreciate any help.