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Old 06-20-2010, 11:16 PM   #58
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

Originally Posted by agc View Post
I'd like to run FastQC on SOLiD reads. I saw that someone did this using solid2fastq. Is it possible to do it without running solid2fastq? IE, would it work with only the SOLiD 'quals' file?
It will work with colorspace fastq files - you don't need to convert to base calls. I don't work with SOLID data directly so I'm not sure whether this is produced directly by the pipeline or not. I'm happy to look at other alternatives for SOLID data, but the program is fairly tied to fastq format (ie needs to work with a sequence and an encoded quality string).

Originally Posted by agc View Post
EDIT: After running FastQC on SOLiD files converted to fastq files via solid2fastq, the results file says (under basic statistics):
File type Conventional base calls

Should it have recognized it as colorspace?
It depends on the conversion. If you look in the file you'll either see conventional base calls (something like GATCTCTAGATCTCT) or colorspace calls (something like G1324132431432434312). If you see colorspace calls and the report says conventional calls then can you send me the top few lines of the file and I can see why it's going wrong. It may be that your conversion program converted to base calls already though.

It FastQC gets the file type wrong it's normally pretty obvious since most of the graphs will show very weird results.
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