This is a test version of Biostars. For the public version, visit https://www.biostars.org.
When to remove duplicates

I followed this paper "Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks" in Nature Protocol to analyze RNA seq data.

In this paper, it does not remove duplicate by SAMTOOLS or Piscard.

But in other pipelines, I saw people do it.

My question is when to remove duplicates and it is OK to follow the pipeline in this paper without removing duplicates?

I want to select the genes with differential expressions from RNA-Seq data.

rna-seq
• 2,802 views • link
updated by harold.smith.tarheel harold.smith.tarheel • written by jolin0701-dy jolin0701-dy

Hello jolin0701-dy!

Duplicate post! This questions has been asked before.

For this reason we have closed your question. This allows us to keep the site focused on the topics that the community can help with.

• 0 views • link
written by User 59 User 59

2 answers

It think it's commonly not advisable to remove duplicates in RNA-seq. In highly expressed genes it may be impossible to distinguish duplicates from truly separately sequenced molecules.

• 0 views • link
written by WouterDeCoster WouterDeCoster

Duplicates are removed when they're likely to be PCR artifacts (e.g., moderate coverage WGS), and those artifacts will affect your analysis (e.g., variant calling). Duplicates in RNA-Seq are more likely the product of high-abundance transcripts and should not be removed.

• 0 views • link
written by harold.smith.tarheel harold.smith.tarheel

Log in to answer this question.

More posts like this