I'm trying to establish a rna-seq workflow to analyse a bacterial transcriptomics, however, when i run the cufflinks module with the annotations there is none fpkm values associated to the data. I'd like to know what I can change to correct it. Thanks in advance.
Examining the value for "FPKM_status" (column 13: http://cole-trapnell-lab.github.io/cufflinks/file_formats/index.html#fpkm-tracking-format) can reveal what the problem is in some cases.
If the coverage is shallow, go back and examine the inputs. Double check that the fastq inputs are in fastqsanger format and that datatype is assigned - when this is wrong, poor mapping can result. If using a reference annotation file (GTF, GFF3), double check that the chromosome identifiers are an exact match for those in the reference genome used for mapping. You might also want to see what results can be had by not using a reference annotation dataset at this stage (it can be introduced in Cuffmerge, then those results given to Cuffdiff). Sorting of the BAM input when using Bowtie (if used) instead of Tophat is important - when not done, this can also lead to problems, but these generally result in a error when using Galaxy.
Related help is in this prior post: Cufflinks output file with many 0 FPKM values
Thanks, Jen, Galaxy team