Hello Jianguang,
The tool NGS: QC and manipulation - FASTQ Groomer has some
information about this, including a link to a wikipedia entry with more
details specifically about the SRA:
http://en.wikipedia.org/wiki/FASTQ_format
http://en.wikipedia.org/wiki/FASTQ_format#NCBI_Sequence_Read_Archive
And here is the SRA submission form, although the experimental record
you downloaded from is the best place to find details:
https://www.ebi.ac.uk/ena/about/sra_data_format
SRA accepts CS and Fastq. In Galaxy these translate to:
Color space reads:
- datatype Color Space Sanger
- annotated as fastqcssanger
Fastq reads:
- datatype with Phred quality offset 64 Illumina 1.3-1.7
- annotated as fastqillumina
and
- datatype with Phred quality offset 33 Illumina 1.8+
- annotated as fastqsanger
Many tools require fastqsanger. Use the FASTQ Groomer to transform
as needed, but double check with FastQC just like you are doing. I have
seen data labeled as Illumina 1.5 that was really already scaled to
Phred+33, or at least appeared to be. In the end this is a judgement
call or you can try to contact SRA/data authors for a definitive answer
if there are no processing notes in the experiment (often the case).
Hopefully this helps,
Jen
Galaxy team
On 3/5/13 8:18 AM, Gene Genome wrote:
Hi all,
Please help with the quality score type for the downloaded Solid
datasets. I downloaded RNA-seq datasets, which were generated by AB
Solid system, as base space and at FastQ format from SRA of NCBI. I
uploaded the datasets onto the online sever Galaxy and change the
datatype directly into fastqsanger and then test the quality by
running FastQC. The output per base quality of solid dataset (please
take look at the attached figure per_base_quality-Solid) is quite
different from the output per base quality of Illumina dataset (please
compare with the attached figure per base quality-Illumina). The top
score for Solid dataset is about 31, however the top score for Illumina
dataset is 38. What is the quality score type for the downloaded Solid
datasets when downloaded as base space and at FastQ format from SRA of
NCBI? Please help me solve this problem.
Thanks.
Best regards.
Jianguang Du
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