Question: How many input BAM files for Cuffquant?
0
wmorgan • 0 wrote:
I'm trying to use the Cufflinks v. >2.2.0 workflow, which uses Cuffquant. The Cufflinks documentation says that "Cuffquant takes as input a single SAM/BAM file of aligned reads and a single GTF/GFF file of gene annotations." However, running Cuffquant at usegalaxy.org gives the option to add replicates, so I added the BAM files of my replicates (e.g., three for the control samples). Cuffquant ran fine for both the control and experimental, but when I tried to use the two .cxb output files in Cuffdiff, I got a warning that "No conditions are replicated...", indicating that Cuffdiff didn't recognize that replicates were entered into Cuffquant. So should I run Cuffquant with each BAM file from Tophat separately?