I am running cuffdiff but I have a doubt with the -b option
According to the manual
-b "Providing Cufflinks with the multifasta file your reads were mapped to via this option instructs it to run our bias detection and correction algorithm which can significantly improve accuracy of transcript abundance estimates"
I mapped my reads ( illumina-single end) with hisat2 to one index from the genome.fa (the whole genome), not from an index of a multi fasta genome.
So in -b option my input is the genome.fa (whole genome) or I have to do a multi fasta from my genome.fa