Hi Jeremy,

I tried to run cufflinks to assemble transcripts after running Tophat against 
my own reference. This error was encountered.

What was wrong?  How to fix it?

Error running cufflinks. [21:01:14] Inspecting reads and determining fragment 
length distribution.
Processed 11130 loci.
Warning: Using default Gaussian distribution due to insufficient paired-end 
reads in open ranges.  It is recommended that correct paramaters 
(--frag-len-mean and --frag-len-std-dev) be provided.
> Map Properties:
>       Total Map Mass: 224153.00
>       Read Type: 50bp single-end
>       Fragment Length Distribution: Truncated Gaussian (default)
>                     Default Mean: 200
>                  Default Std Dev: 80
[21:01:18] Assembling transcripts and estimating abundances.
Processed 11130 loci.
[21:01:22] Loading reference annotation and sequence.
No fasta index found for ref.fa. Rebuilding, please wait..
Error: sequence lines in a FASTA record must have the same length!

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