Dear Noa,

Can you please  tell me the parameters that I should keep while mapping
bacterial transcripts using cuffkins. I have kept the default parameters as
in Cufflinks and used my custom genome annotation  in gff3 format. The
cufflinks seems to work Ok but all the FPKM values in these files are zero.
As suggested by other users I have checked the correctness of my GFF3
files. The corresponding fasta file was used for mapping the transcripts
using Bowtie. Are there any special trick for mapping bacterial
transcriptome.

regards,

Bomba
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