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Old 03-13-2014, 07:27 AM   #1
super0925
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.
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Old 04-16-2014, 04:26 PM   #2
mbzmg1
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Location: Colorado

Join Date: Feb 2012
Posts: 9
Default

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:
/results/analysis/output/Home/NAME_OF_RUN/

and the .fastq files at:
/results/analysis/output/Home/NAME_OF_RUN/plugin_out/downloads/

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

Hope this helps.
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Old 04-17-2014, 12:33 AM   #3
Jeremy
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Location: Pathum Thani, Thailand

Join Date: Nov 2009
Posts: 190
Default

bamtools convert can convert bam to fastq
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