I am hoping that someone might be able to give me some advice on adjusting or controlling for batch effects in RNA-Seq data using Ballgown?
I have got RNA-seq data for different batches of sequencing for the replicates of the sample. I followed new tuxedo pipeline for my preliminary analysis of the data and found that there were difference in total number of PE reads between the two batches of the sequencing (batch 1: 27 million reads; batch 2: 20 million reads)- therefore I think this difference could be due to batch effects within my dataset.
Is it possible to control for batch effects within Ballgown pipeline using the stattest function?
Any advice on this would be gratefully appreciated!