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Question: Working with FASTQ files from Ion Proton
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gravatar for avnairn
4.5 years ago by
avnairn • 0
United States
avnairn • 0 wrote:

Hello,

I am trying to use a FASTQ file of RNA-Seq results from an Ion Proton Sequencer.  The FASTQ file seems to have uploaded fine, but it doesn't show up in the "FASTQ" file list for Tophat2 and other programs.  I read about the FASTQ groomer and tried running that using the "Sanger&Illumina" option but got an error message which I could only read part of.  Should I have chosen one of the other platform options or is there some other way to convert the data so that I can use the data in Galaxy?

Any help would be appreciated!

Thanks,

Alison

 
rna-seq • 2.2k views
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modified 4.5 years ago by Bjoern Gruening ♦ 5.1k • written 4.5 years ago by avnairn • 0
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gravatar for Bjoern Gruening
4.5 years ago by
Bjoern Gruening ♦ 5.1k
Germany
Bjoern Gruening ♦ 5.1k wrote:

Hi Allison,

uploaded fastq files will be recognised as 'fastq' format. TopHat and others only take as input 'fastqsanger' files. If you are sure you uploaded file is in the 'sanger' encoded fastq format you can easily change the filetype of your dataset to 'fastqsanger'. Otherwise, you can convert your fastq file to the sanger format with the 'fastq groomer'.

Read more about managing datsets in Galaxy here:

https://wiki.galaxyproject.org/Learn/ManagingDatasets?action=show&redirect=Learn%2FManaging+Datasets

About the fastq format here:

http://en.wikipedia.org/wiki/FASTQ_format

And about the grooming step, if really needed in the Galaxy wiki: https://wiki.galaxyproject.org/Support#Dataset_special_cases

The link above includes a link to a Vimeo video Jennifer made that walks-through the processing step-by-step.

Ciao,

Bjoern
ADD COMMENT • link written 4.5 years ago by Bjoern Gruening ♦ 5.1k
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