Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
help to extract data zion22 Bioinformatics 0 01-05-2019 03:38 PM
Removing overrepresented sequences (rRNA contaimation) from RNAseq raw data nandr009 Bioinformatics 1 11-30-2018 05:54 AM
can small rnaseq data be analyzed like rnaseq data? PFS Bioinformatics 5 05-02-2017 08:16 AM
Extract most squenced region from RNAseq Piggy Bioinformatics 1 11-11-2016 08:42 AM
rRNA removal for RNAseq analysis genomica Bioinformatics 1 03-21-2016 12:31 PM

Thread Tools
Old 09-04-2020, 04:51 AM   #1
Junior Member
Location: Norway

Join Date: Sep 2020
Posts: 3
Default Extract rRNA from RNASeq data

Hi everyone,
I'm new here and my searches didn't quite give me what I wanted so hopefully this isn't an already answered question. Any help is greatly appreciated.

I have some single end RNAseq data from a patient sample and I need to perform variant calling from specifically on the rRNAs. I would like to know what is the best method to extract the rRNA to perform the analysis. From what I have gathered, using STAR aligner and then using GATK tools to do the variant callings seems to be the best strategy.

Some background:
The original designers of the project hypothesise that there's potentially an error in the polymerase of the patient that causes error in the production of the rRNA. They have sequenced the total RNA but unfortunately, the sequencing company did their usual protocol and depleted the rRNA. But they suspect that there's at least some degree of rRNA left which can at least indicate if there's any indication for having variation in the rRNA sequences.
josh_OUS is offline   Reply With Quote
Old 09-04-2020, 09:09 AM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,125

You can use the "filter" mode for "" from BBMap suite for this. Download the human rDNA repeat sequence. Reads that match rDNA can be filtered away from your data. A guide to use bbduk is available here.

If most of rRNA has been depleted from your sample there is not much you can do.
GenoMax is offline   Reply With Quote
Old 09-06-2020, 11:05 PM   #3
Junior Member
Location: Norway

Join Date: Sep 2020
Posts: 3

Thanks for the input! I'll look into this and see if I can salvage anything
josh_OUS is offline   Reply With Quote

rnaseq, rrna

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 03:28 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO