Go Back   SEQanswers > Applications Forums > Sample Prep / Library Generation

Similar Threads
Thread Thread Starter Forum Replies Last Post
tRNA and rRNA depletion ramsemm RNA Sequencing 1 06-15-2018 01:43 AM
Could I filter rRNA and tRNA by using Tophat or Cufflinks?? mart555 Bioinformatics 36 12-17-2014 06:35 PM
filter sequences from rRNA, tRNA cascoamarillo Bioinformatics 8 01-29-2013 11:13 AM
tRNA/5S rRNA depletion mateo Sample Prep / Library Generation 4 01-26-2012 02:48 PM
tRNA contamination Newie RNA Sequencing 0 01-08-2011 06:40 AM

Thread Tools
Old 03-19-2014, 02:52 PM   #1
Junior Member
Location: ithaca

Join Date: Jan 2014
Posts: 8
Default rRNA & tRNA contamination in whole genome sequencing

Hi folks

I had a peculiar phenomenon happening with my genome reqsequencing project and was wondering if other people have seen this.

I've been using Qiagen's DNeasy kit to isolate Drosophila DNA and submitted for whole genome sequencing on a Illumina Hiseq2500 platform (Truseq for library prep).

This is a reference based genome resequencing project and I've been reassembling some of the bacteria genome that lives inside the fly and what was strange with my alignment was that I was getting alot of false alignments only around the rRNA and tRNA genes. The coverage doubles around the rRNA and tRNA genes and the only explanation I had was the secondary structure or the sheer massive amounts of those nulceotides had survived the RNase treatment.

Have people seen this before? And are there recommended protocols to decrease the amount of rRNA and tRNA in your DNA sample?
choijae3 is offline   Reply With Quote

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 09:12 PM.

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