I am performing differential gene expression analysis between "control" and "treated" samples that differ 2-3 fold in their depth (control samples are half to one third in number of reads as compared to treated samples). If I perform DE analysis using the old Tuxedo protocol, I do not observed many differentially expressed genes. Not even those that have been used for sample validation before subjecting them for sequencing.
If I load
Bigwig files (relatively better normalized) for these samples onto the genome browser, I can see expected difference in reads on the genes of interest. In order to normalize samples for the depth of sequencing, I am trying
Samtools view -s to subset the .bam files of samples to similar sizes. But these subset files ain't compatible with
Cufflinks since they lack the EOF marker.
I am wondering if such normalization is a good idea and if yes, how to get around this problem of incompatibility with
Thanks a lot for your help in advance!