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!
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!
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