Can I analyze single-end and paired-end RNA-Seq data together?
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!
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pinheirofabiano •
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roxana •
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roxana •
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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.
I agree with @genomax... read about batch effect and its consequences in RNA-Seq analysis..