SEQanswers

Go Back   SEQanswers > Applications Forums > RNA Sequencing



Similar Threads
Thread Thread Starter Forum Replies Last Post
De novo genome assembly question: which assembly should I use? tarias Bioinformatics 1 12-07-2018 04:23 AM
Compare de-novo transcriptome assembly to genome reference guided assembly IdoBar Bioinformatics 1 04-04-2014 12:28 AM
Inquiry: minimum length of reads for referece-based assembly or de novo assembly sunfuhui Bioinformatics 1 10-04-2013 09:28 AM
Lexogen announces the "Win your SENSE Study" award lexogen Vendor Forum 1 04-25-2013 06:36 AM

Reply
 
Thread Tools
Old 10-16-2019, 09:01 AM   #1
Vinn
Member
 
Location: Sweden

Join Date: Nov 2014
Posts: 18
Default Lexogen SENSE for de novo assembly?

Hi folks

I wonder if anyone would like to share experience with Lexogen SENSE for de novo assembly? I am considering using the kit as it can deal with much lower RNA input (some of my samples have total RNA ca. 50 ng), but I have never tried the kit before. I am working with tree species with a genome (but not annotation) available. I am thinking about doing genome-guided de novo assembly.

Thanks in advance! Any comments and suggestions are welcome!
Vinn is offline   Reply With Quote
Old 01-09-2020, 01:09 AM   #2
lexogen
Registered Vendor
 
Location: Vienna, Austria and NH, USA

Join Date: Aug 2012
Posts: 49
Default

Dear Vinn,
I came across your posting and hope this input helps you and others:

Lexogen's SENSE kit has been used for de novo assembly in at least these three publications:

Rizzo, Paride; Altschmied, Lothar; Stark, Pauline; Rutten, Twan; Gündel, André; Scharfenberg, Sarah et al. (2019): Discovery of key regulators of dark gland development and hypericin biosynthesis in St. John's Wort (Hypericum perforatum). In Plant Biotechnology Journal. DOI: 10.1111/pbi.13141.

Dinh Chieu, Hoang; Suwansa-Ard, Saowaros; Wang, Tianfang; Elizur, Abigail; Cummins, Scott F. (2019): Identification of neuropeptides in sea cucumber Holothuria leucospilota. In General and comparative endocrinology, p.*113229. DOI: 10.1016/j.ygcen.2019.113229.

Gault, Christine M.; Kremling, Karl A.; Buckler, Edward S. (2018): Tripsacum De novo Transcriptome Assemblies Reveal Parallel Gene Evolution with Maize after Ancient Polyploidy. In The Plant Genome 11 (3). DOI: 10.3835/plantgenome2018.02.0012.

Any further questions, comments (and of course, results!) please also direct to info@lexogen.com.

Thank you,
Lukas Paul

Sr. Mgr. Scientific Affairs
Lexogen GmbH
lexogen is offline   Reply With Quote
Reply

Tags
de novo assembly, lexogen sense, rna-seq

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 06:45 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO