SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Ion Torrent



Similar Threads
Thread Thread Starter Forum Replies Last Post
Ion torrent data analysis microbasa Ion Torrent 0 06-13-2015 01:21 AM
Using TopHat2 RNA-Seq Data IOn-Torrent mpalegre RNA Sequencing 3 12-09-2014 01:05 PM
Chip-SEq Data Analysis. S. cerevisiae.IOn-Torrent mpalegre Bioinformatics 1 02-19-2014 08:48 AM
Ion Torrent Data Analysis RonanC Ion Torrent 2 08-07-2012 04:55 PM

Reply
 
Thread Tools
Old 12-04-2017, 07:48 AM   #1
bvk
Member
 
Location: USA

Join Date: May 2015
Posts: 56
Default Tools for Ion Torrent RNA-Seq data analysis

Hello Everyone,

I'm aware about the tools that need to be used for RNA-Seq data analysis of illumina platform.

But I would like to know what tools need to be used for RNA-Seq analysis of Ion Torrent platform?

For alignment I know that BBMap is faster and does better job. May I know which tools need to be used for the other steps and differential analysis.

Thank you
bvk is offline   Reply With Quote
Old 12-04-2017, 08:20 AM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,585
Default

Tools for Illumina should be fine to use for Ion Torrent data as well since you still have fastq data. There may be biases/other issues with Ion torrent that you would need to keep in mind (e.g. homo-polymers) but otherwise use any tools you like.
GenoMax is offline   Reply With Quote
Old 12-04-2017, 08:25 AM   #3
bvk
Member
 
Location: USA

Join Date: May 2015
Posts: 56
Default

Thanks for the reply. But I see that Tophat and cufflinks pipeline cant be used for Ion torrent data right. Are you sure that I can use these tools?

Can I also use Hisat2, Stringtie and Ballgown?

Some were saying that BBMap is good for alignment for Ion Torrent data.
bvk is offline   Reply With Quote
Old 12-04-2017, 08:57 AM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,585
Default

It is not that it can't be used. It is more that you should not be using TopHat pipeline for any new data. TopHat is in maintenance mode and even its developers recommend that you use HISAT2, their latest creation.

You may need to try a newer aligner (e.g. BBMap, STAR, HISAT2) and see what works best for your data.
GenoMax is offline   Reply With Quote
Old 12-05-2017, 09:39 AM   #5
bvk
Member
 
Location: USA

Join Date: May 2015
Posts: 56
Default

Thank you !! Our data is generated from Ion Torrent Amplicon based platform. Do you think Hisat can be used for that? And could you please tell what is the main difference between Ion torrent amplicon and Illumina platform data?
bvk is offline   Reply With Quote
Old 12-05-2017, 10:02 AM   #6
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,585
Default

Are you referring to targeted amplicon sequencing for RNAseq?
GenoMax is offline   Reply With Quote
Old 12-06-2017, 12:19 AM   #7
bvk
Member
 
Location: USA

Join Date: May 2015
Posts: 56
Default

Yes it is Ion Torrent Amplicon Sequencing RNA-Seq. I see that TMAP is the best alignment tool for this data. I would like to know how to do the quantification and how to get the gene-level read counts with this data.

And also could you please tell me what is the exact difference between Illumina and Ion Torrent amplicon based platforms from biology point of view.

Last edited by bvk; 12-06-2017 at 12:26 AM.
bvk is offline   Reply With Quote
Old 12-06-2017, 09:54 AM   #8
bvk
Member
 
Location: USA

Join Date: May 2015
Posts: 56
Default

Ok. Differences between platforms is found here.

Thank you

Last edited by GenoMax; 12-06-2017 at 10:42 AM. Reason: Fixed article URL
bvk is offline   Reply With Quote
Old 12-11-2017, 09:26 AM   #9
snetmcom
Senior Member
 
Location: USA

Join Date: Oct 2008
Posts: 153
Default

Quote:
Originally Posted by bvk View Post
Yes it is Ion Torrent Amplicon Sequencing RNA-Seq. I see that TMAP is the best alignment tool for this data. I would like to know how to do the quantification and how to get the gene-level read counts with this data.

And also could you please tell me what is the exact difference between Illumina and Ion Torrent amplicon based platforms from biology point of view.
The Ampliseq RNA panels just use tmap and the torrent suite coverage analysis tools. I don't think these libraries should be analyzed as RNAseq data as they are specifically targeted for exons.
snetmcom is offline   Reply With Quote
Reply

Tags
iontorrent, rnaseq, tools and techniques

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 08:36 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO