I’m considering using Cuffquant to quantify the BAM files in parallel, in order to speed up the process.
Originally, Cuffdiff has the following steps before the “Testing for differential expression and regulation in locus” step:
“Inspecting maps and determining fragment length distributions”; “Modeling fragment count overdispersion”; “Calculating preliminary abundance estimates”; “Learning bias parameters”.
So in the new workflow, what steps in the above list does Cuffquant cover?
Which of the above steps are still performed in Cuffdiff if running Cuffquant first?
Currently, our “Inspecting maps and determining fragment length distributions” step takes an extremely long time for 6 BAM files. I’m wondering if running Cuffquant on these 6 BAM files individually (with some parallel processing) could help speed up this step?
Any ideas and advice would be greatly appreciated.
Thank you very much!