Ion Torrent FastQ Analysis on Galaxy

[HeidiJTP]

I have two questions about analyzing PGM FastQ files using Galaxy.

1) Can someone confirm if Ion Torrent FastQ files are in Sanger format?

I believe they are based on information from the wiki page: http://en.wikipedia.org/wiki/FASTQ_format

My FastQ files do not have lowercase letters, and they contain !" characters.


2) Is it normal to have to rerun FASTQ Groomer after each step in Galaxy?

I ran FASTQ Groomer on my complete dataset. Then I ran a barcode splitter, after which it seems that I have to run FASTQ Groomer again on each file before I can process them any further. Is this normal or does it indicate an error? This is what made me question whether I was correct in specifying Sanger format.

Thanks for any feedback!

[JackieBadger]

If you specify the exact input file coding you wont have to run groomer multiple times

[GenoMax]

2) Is it normal to have to rerun FASTQ Groomer after each step in Galaxy?

I ran FASTQ Groomer on my complete dataset. Then I ran a barcode splitter, after which it seems that I have to run FASTQ Groomer again on each file before I can process them any further. Is this normal or does it indicate an error? This is what made me question whether I was correct in specifying Sanger format.

Thanks for any feedback!

You should not need to run groomer over again. In case the metadata is wrong up you can choose the "pencil" icon next to the dataset name and manually set the file type to "fastqsanger".

[HeidiJTP]

Thanks for the help! I changed it to "fastqsanger" under Datatype as suggested, and this seems to have done the trick so that I don't need to rerun FASTQ Groomer.

Can anyone verify that Sanger is the format used by Ion Torrent?

[GenoMax]

Can anyone verify that Sanger is the format used by Ion Torrent?

http://en.wikipedia.org/wiki/Fastq#Quality

http://mendel.iontorrent.com/ion-doc...e_6128102.html Look at the "Results" section at the bottom of the page.

[HeidiJTP]

Thanks GenoMax! And I appreciate that you included the documentation from Ion Torrent.