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!

Thanks

Jiannong