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super0925 03-13-2014 07:27 AM

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.

mbzmg1 04-16-2014 04:26 PM

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.

Jeremy 04-17-2014 12:33 AM

bamtools convert can convert bam to fastq

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