Need help about depth difference of biological replicate

[linda sandebarg]

Hi, I am very novice about statistics and data analysis. Recently we have done some RNA sequencing with RNA-tag sequence where we pool many samples in tube for library preperation. We did Hiseq 2500 but after demultiplixing we see huge difference between biological replicate. One experiment looks like this COntrol: A- 1miilion, B-5million, c 0.8 million Treatment: A-3 million, B- 5 million, C 12 million. In a word there is a huge depth variation among biological replicate, i am working with bacteria. Can I use this data for differential expression or should re do the sample. Please help a poor phd!!!!