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Question: fastq data types
1
gravatar for tomaz
4.2 years ago by
tomaz • 10
tomaz • 10 wrote:

Hi,

I've done quite some searching and have found numerous posts on the fastq format versions. I still cannot figure out what galaxy's format names designate:

- fastqcssanger

- fastqillumina

- fastqsanger

- fastqsolexa

Any help would be greatly appreciated.

 
fastq datatype formatting galaxy tools • 1.4k views
ADD COMMENT • link •
modified 4.2 years ago by Jennifer Hillman Jackson ♦ 25k • written 4.2 years ago by tomaz • 10
4
gravatar for Peter Cock
4.2 years ago by
Peter Cock • 1.4k
European Union
Peter Cock • 1.4k wrote:

See http://dx.doi.org/10.1093/nar/gkp1137

  • fastqcssanger = FASTQ color space using Sanger encoding (PHRED scores + 33)
  • fastqillumina = FASTQ using now obsolete Illumina encoding (PHRED scores + 64)
  • fastqsanger = FASTQ using Sanger encoding (PHRED scores + 33), probably you want this
  • fastqsolexa = FASTQ using long obsolete Solexa encoding (Solexa scores + 64)
ADD COMMENT • link modified 4.1 years ago • written 4.2 years ago by Peter Cock • 1.4k

Great answer Peter. I'm going to add in a link here that will help others (reading or finding post through a search) to detect original formatting and modify as needed for use with Galaxy's tools (or most of them!). The above is right on target; ".fastqsanger" is the standard quality score scaling expected by most tools.
http://wiki.galaxyproject.org/Support#Dataset_special_cases
Best, Jen, Galaxy team

ADD REPLY • link written 4.2 years ago by Jennifer Hillman Jackson ♦ 25k
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