Can I analyze single-end and paired-end RNA-Seq data together?

Question

[roxana]

Hi everyone,

I'm working on my thesis titled "Comprehensive Analysis of Gene Expression Profiles to Identify Prognostic Factors in Primary and Metastatic Breast Cancer." I have two RNA-Seq datasets: one prepared using single-end sequencing (SE) and the other using paired-end sequencing (PE).

Is it feasible to analyze these datasets together, or should I ensure both datasets use the same LibraryLayout? Any advice on handling this would be greatly appreciated!

Thank you!

[GenoMax]

You could only use read 1 from PE dataset and make both single-end equivalent. Keep in mind that mixing two datasets can be tricky since there may be biases that you can't account for in your analysis.

[pinheirofabiano]

I agree with @genomax... read about batch effect and its consequences in RNA-Seq analysis..