Dear Noa,<br><br>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. <br>
<br>regards,<br><br>Bomba<br>