Go Back   SEQanswers > Sequencing Technologies/Companies > Ion Torrent

Similar Threads
Thread Thread Starter Forum Replies Last Post
GATK recalibration confused, one step or two step? frankyue50 Bioinformatics 2 11-25-2013 03:25 PM
ChIp seq Library : control and step frigo Illumina/Solexa 5 10-28-2011 08:58 AM
advice on the size selection step in ChIP-seq protocol mboth Sample Prep / Library Generation 5 10-13-2011 02:59 AM
step by step for rarefaction calculation psong Metagenomics 1 01-06-2010 06:08 AM

Thread Tools
Old 03-13-2014, 07:27 AM   #1
Senior Member
Location: UK

Join Date: Feb 2014
Posts: 206
Default The first step on RNA-Seq

Hi All

Hi I have got my raw data from biologist who running sequencing on Proton. I need to get the .fastq reads for downstreaming analysis (e.g. QC control, Alignment , DE analysis...) on Torrent Server by command line. I don't know that if Proton could output .fastq directly.

I found that on Torrent Browser there is a panel called 'select a plugin to run'

if I click 'FileExporter' ,there are 4 options

Create SFF?

Create FASTQ?

Include Variant Caller Files (if available)?

Zip results?

If I select 2 and 4 and submit, there is not any response

Btw, if I don't use Browser and use Torrent Server to run command line, how could I do it. I mean I don't know how to run FileExporter in Command line ,what is input and output?

Thank you!

Sorry this has been sorted cos is my plugin version's problem.

Last edited by super0925; 03-14-2014 at 07:54 AM.
super0925 is offline   Reply With Quote
Old 04-16-2014, 04:26 PM   #2
Junior Member
Location: Colorado

Join Date: Feb 2012
Posts: 9

The default output format for Ion Torrent is .bam (even if not mapping the reads).

You need to fill out the settings for the FileExporter plugin before it will generate the .fastq files correctly.

You will find the .bam files at:

and the .fastq files at:

(this is for the current version of TSS and may change with updates)

Hope this helps.
mbzmg1 is offline   Reply With Quote
Old 04-17-2014, 12:33 AM   #3
Senior Member
Location: Pathum Thani, Thailand

Join Date: Nov 2009
Posts: 190

bamtools convert can convert bam to fastq
Jeremy 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 07:20 PM.

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