How to process and analyze Total RNA-Seq data?
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@mohammedtoufiq91-17679
Last seen 1 hour ago
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Hi,

I have a question about analyzing Total RNA-Seq data. The lab has generated Total RNA-Seq this time to study including lncRNAs in Inflammatory Bowel Disease. Ideally, for mRNA-Seq I usually use either EdgeR or DESeq2 based on the analysis requirements followed by customized gene enrichment and biological pathways analysis.

I usually start with the raw counts data in the mRNA-Seq, similarly the same been provided for the total RNA-Seq too. Are the processing/normalization and analysis steps of total RNA-Seq are similar to the mRNA-Seq analysis. Are there any additional customizations needed?

Thank you,

Best Regards,

Toufiq

DESeq2 R edgeR Normalization RNASeq • 126 views
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@gordon-smyth
Last seen 59 minutes ago
WEHI, Melbourne, Australia

edgeR analyses read counts. As long as you can allocate reads to genes, then the analysis pipeline is the same.

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Gordon Smyth thank you for the response. Yes, I have read counts where genes as rows and samples as columns.

Additionally, does edgeR has any functionality that would map genes to classify coding or non coding genes. Thank you.