Merging PE reads before de novo RNA-Seq assembly

roussine

Arctic Member

Join Date: Nov 2017

Posts: 2
- Share
- Tweet
#1

Merging PE reads before de novo RNA-Seq assembly

01-25-2018, 08:39 AM

Hello!
can someone please give an opinion: does that make sense to merge PE reads before a de novo RNA-seq assembly (say with Trinity)?
Merging tools are quite fast (like USEARCH www.drive5.com/usearch/manual/merge_pair.html), and the amount of raw data is reduced drastically. Can merged data be suitable for further assembly in a “single-ends” mode, or am I missing some theory behind it?.. Seems like it may save a lot of computations.

Thanks in advance.
Leo
Tags: assembly, pe reads, rna-seq, trinity, usearch
GenoMax

Senior Member

Join Date: Feb 2008

Posts: 7142
- Share
- Tweet
#2

01-25-2018, 09:38 AM

For reference cross-posted to: https://www.biostars.org/p/295213/
Comment
pmiguel

Senior Member

Join Date: Aug 2008

Posts: 2328
- Share
- Tweet
#3

01-26-2018, 04:11 AM

I've never understood why people think that pair-merging prior to de novo assembly is a good idea. Seems like were that the case, assembly engines would just do pair-merging themselves prior to other assembly steps.

--
Phillip
Comment

Previous template Next

Cancer Drug Resistance: The Lingering Barrier to Rising Survival

by SEQadmin2

Cancer survival rates have significantly increased in the last few decades in the United States, reaching a combined 70% 5-year survival rate by 2021. Behind this number, there are years of research to find new therapies, drug targets, and early detection methods. But there is one core challenge that keeps slowing down these advances, and it’s about drug resistance.

There is no single reason why many patients don’t respond to treatment as expected. Cancer is...
- Channel: Articles
Yesterday, 05:17 AM
Reply to Nine Things a Sample Prep Scientist Thinks About Before Sequencing

by GATTACAT

Love this - good data definitely starts from good input, and poor input can only give relatively poor data. I particularly like the mention of Nanodrop/absorbance based methods for quantification. It's such a toss up if you'll get an accurate reading or what amounts to a randomly generated number, and a lot of library/sequencing related issues can be traced back to poor quant.
- Channel: Articles
07-01-2026, 11:43 AM
Nine Things a Sample Prep Scientist Thinks About Before Sequencing

by SEQadmin2

I’m not a sequencing expert. I’m a purification scientist who uses NGS to evaluate workflows my group develops. With this perspective, we think about the sample first and the NGS workflow second. The sequencer is an exceptionally honest reporter, but it can only report on what you give it, so whether you get clean, interpretable data from an NGS workflow is largely determined before you begin.

Here are nine questions we think about, in roughly the order they matter, before...
- Channel: Articles
06-18-2026, 07:11 AM

Topics	Statistics	Last Post
Genome-Wide CRISPR Screen Uncovers Unlikely Psoriasis Target by SEQadmin2 Started by SEQadmin2, Yesterday, 10:08 AM	0 responses 6 views 0 reactions	Last Post by SEQadmin2 Yesterday, 10:08 AM
Engineered Protein Motor Takes Its First Steps Along DNA Track by SEQadmin2 Started by SEQadmin2, 07-07-2026, 11:05 AM	0 responses 8 views 0 reactions	Last Post by SEQadmin2 07-07-2026, 11:05 AM
High-Resolution Sequencing Exposes Hidden Toxoplasma Diversity by SEQadmin2 Started by SEQadmin2, 07-02-2026, 11:08 AM	0 responses 31 views 0 reactions	Last Post by SEQadmin2 07-02-2026, 11:08 AM
New AI Model Captures Long-Range Genomic Signals to Improve RNA Splice Site Prediction by SEQadmin2 Started by SEQadmin2, 06-30-2026, 05:37 AM	0 responses 29 views 0 reactions	Last Post by SEQadmin2 06-30-2026, 05:37 AM

Unconfigured Ad

Merging PE reads before de novo RNA-Seq assembly

Comment

Comment

Latest Articles

ad_right_rmr

News