Hi Everyone,
We use cufflinks and tophat for our RNA-seq analysis. In our previous protocol, we use FASTX collapser to collapse reads with same sequence into one before doing alignments using bowtie/tophat. Does cufflinks consider such files when calculating FPKM?
Thanks,
We use cufflinks and tophat for our RNA-seq analysis. In our previous protocol, we use FASTX collapser to collapse reads with same sequence into one before doing alignments using bowtie/tophat. Does cufflinks consider such files when calculating FPKM?
Thanks,