SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Ion Torrent



Similar Threads
Thread Thread Starter Forum Replies Last Post
why low mapping rates for RNAseq? NGSfan RNA Sequencing 49 09-09-2014 12:34 PM
Low mapping rate for RNAseq 2x150 trimmed data Markovia Bioinformatics 0 08-30-2013 06:55 PM
Transcriptomics RNASeq + Microarray dataset rmflight Bioinformatics 1 12-13-2012 11:27 PM
best RNAseq mapping tool for bacteria sissi Bioinformatics 6 03-05-2012 03:48 PM
RNAseq - low cluster density - possible inhibitor? OnUrMark Sample Prep / Library Generation 11 05-07-2011 07:05 PM

Reply
 
Thread Tools
Old 01-29-2014, 07:31 AM   #1
Gorbenzer
Member
 
Location: italy

Join Date: Apr 2012
Posts: 45
Exclamation Bacteria transcriptomics RnaSeq - low output

Hi everyone,
we are testing the v2 RnaSeq kit for IonTorrent in order to do some bacteria transcriptomics.

During library preparations all quality values seems good but when we sequence the output is really low: 20/25 Mbp with three samples in a 314 chip with 60% polyclonals. It seems that the one touch/beads enrichment is the problematic step.

Anyone have any suggestion or modified protocol in order to improve the output?


Just another question: Anyone have suggestion for rRNA depletion using genus specific probes? We need to improve rRNA deplation for the bacteria genus we study because universal (E. coli based?) rRNA depletion methos don't work well for us, expecially for 23S.

Thanks for the help!
Gorbenzer is offline   Reply With Quote
Reply

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 03:06 AM.


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