SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Merging reads for denovo assembly Niranjanks De novo discovery 1 05-18-2016 10:09 AM
Inquiry: minimum length of reads for referece-based assembly or de novo assembly sunfuhui Bioinformatics 1 10-04-2013 09:28 AM
RNA-Seq: De novo transcriptome assembly of RNA-Seq reads with different strategies. Newsbot! Literature Watch 0 01-10-2012 04:00 AM

Reply
 
Thread Tools
Old 01-25-2018, 07:39 AM   #1
roussine
Arctic Member
 
Location: Arctic

Join Date: Nov 2017
Posts: 1
Default Merging PE reads before de novo RNA-Seq assembly

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
roussine is offline   Reply With Quote
Old 01-25-2018, 08:38 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,784
Default

For reference cross-posted to: https://www.biostars.org/p/295213/
GenoMax is offline   Reply With Quote
Old 01-26-2018, 03:11 AM   #3
pmiguel
Senior Member
 
Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
Posts: 2,290
Default

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
pmiguel is offline   Reply With Quote
Reply

Tags
assembly, pe reads, rna-seq, trinity, usearch

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 11:57 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO