Go Back   SEQanswers > Sequencing Technologies/Companies > Ion Torrent

Similar Threads
Thread Thread Starter Forum Replies Last Post
pipeline for ion torrent data aituka Bioinformatics 11 05-21-2012 05:08 PM
Ion Torrent data quality impressions? rcorbett Ion Torrent 15 03-27-2012 12:43 PM
Metatranscriptome analysis - MiSeq or Ion Torrent? ramsemm Ion Torrent 5 03-06-2012 11:52 AM
GATK and Ion Torrent data NextGenSeb Bioinformatics 2 02-12-2012 09:36 PM

Thread Tools
Old 07-05-2012, 10:20 AM   #1
Junior Member
Location: USA

Join Date: Jul 2012
Posts: 8
Default Ion Torrent Data Analysis

Hi everyone,

I wanted to start a thread to get an idea what other ion torrent users are using/doing for their downstream data analysis. There are a number of preferred software vendors suggested by ion torrent including DNASTAR, Avadis NGS, Partek and NextGENe. Has anyone used these and do you have any recommendations? I am in the process of trying a few of them out and wanted to hear what other people thought.

I suppose whatever software you select depends on the type of work you are doing. I work in a microbiology lab so we will be doing some genome sequencing (so assemblies of genomes and alignments against a reference), RNA-seq (looking at transcript geography and expression levels) and possibly some ChIP-seq. I would be particularly interested to hear from other microbiologists who are doing similar work on the ion torrent but any feedback is welcome.


RonanC is offline   Reply With Quote
Old 08-07-2012, 08:40 AM   #2
Location: Maryland

Join Date: Aug 2011
Posts: 52
You can find Web-Based Training in the link above. Best wishes.
byou678 is offline   Reply With Quote
Old 08-07-2012, 04:55 PM   #3
Junior Member
Location: Edmonton, Canada

Join Date: Aug 2012
Posts: 4
Default also looking for the best way to filter and analyze data

I am trying to detect rare variants in pooled mutated samples. I have barcoded my pools and I have 3 genes I am analyzing in each of 28 pools. Since I am doing this as a test with diluted samples bearing a known mutation I can confirm if the technique is working. I can clearly see the expected mutations (around 2% change), but also see a bunch of sequencing errors, mainly at the end of the reads, which at the end show frequencies close to the real mutation. I been struggling for the last couple of days with SAMtools, CRISP and even the ion torrent variant call plugin without success (this lat one only calls alleles with a minimum of 5% frequency and rare mutations are lower than that. I know there are other Biologist-friendly tools out there, but they are usually expensive, so I am also on the lookout for something free and efficient.

I would mainly like to find a way to tell those sequencing errors from the real variants...any advise?
leogg23 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 05:04 PM.

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