Hi all,

I am trying to assemble a transcriptome using a genome-based approach with tophat2/cufflinks. While tophat2 gives me quite good results (read mapping rate more than 70%) I cannot assemble any transcripts with cufflinks. It doesn't return any specific error, however the number of processed loci equals 0 and the transcripts.gtf file is empty. Below I paste the output of cufflinks and tophat2.

tophat_out/align_summary.txt
Left reads:
          Input     :  36870447
           Mapped   :  26922808 (73.0% of input)
            of these:    288345 ( 1.1%) have multiple alignments (0 have >20)
Right reads:
          Input     :  36870447
           Mapped   :  26995453 (73.2% of input)
            of these:    283619 ( 1.1%) have multiple alignments (0 have >20)
73.1% overall read mapping rate.

Aligned pairs:  25007182
     of these:    267231 ( 1.1%) have multiple alignments
                   43433 ( 0.2%) are discordant alignments
67.7% concordant pair alignment rate.

You are using Cufflinks v2.2.1, which is the most recent release.
[18:36:04] Inspecting reads and determining fragment length distribution.
> Processed 1 loci.                            [*************************] 100%
> Map Properties:
>    Normalized Map Mass: 3198020.00
>    Raw Map Mass: 3198020.00
>    Fragment Length Distribution: Empirical (learned)
>                  Estimated Mean: 182.67
>               Estimated Std Dev: 59.56
[18:37:19] Assembling transcripts and estimating abundances.
> Processed 0 loci.