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
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