Dear Galaxy team
When i ran cuffdiff for my merged transcripts file using a custom reference genome, It ran successfully and i could find significant differences. But i see under the cuffdiff files, it says' couldn't find fasta record for scaffold 1 and scaffold 10, will not be considered for bias correction'.
I checked my reference genome for the respective scaffolds and they are present and i also checked the gtf file and looks like it is represented correctly. I don't know where this messages is coming from and why ?!
I think because of this it doesnt give any FPKM values for genes in those scaffolds which inturn just says NOTEST for these scaffolds. Could you please help me to possibly clear this ?