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Old 11-22-2010, 07:24 AM   #1
Location: US

Join Date: Oct 2010
Posts: 50
Default fastq quality check with Q=33 or Q=64?

Hi all,

I'm trying do quality checking with FASTX toolkit,

Now I'm confused with different fastq. I list some samples as following, Is there anyone know which Q (33/64) I should used for data analysis?

@SRR036482.94 SOLEXA8_1:2:1:0:1735 length=51
+SRR036482.94 SOLEXA8_1:2:1:0:1735 length=51
@SRR036482.95 SOLEXA8_1:2:1:1:1455 length=51
+SRR036482.95 SOLEXA8_1:2:1:1:1455 length=51

Many thanks.
feng is offline   Reply With Quote
Old 11-22-2010, 07:58 AM   #2
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Location: Cambridge, UK

Join Date: Sep 2009
Posts: 625

This definitely looks like Sanger quality values (Phred+33).

See FastQ for more information on the FastQ data format.
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Old 11-22-2010, 12:38 PM   #3
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Location: USA, Midwest

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Posts: 1,178

fkrueger is correct, they are Sanger (Phred+33) encodings. The accession numbers (SRR) indicate that this is data downloaded from the the NCBI SRA. SRA data will always be Phred+33.
kmcarr is offline   Reply With Quote
Old 04-25-2012, 10:39 AM   #4
Location: Brazil

Join Date: Aug 2010
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How are you? There is an excelent paper that describes the FASTQ encoding. But kmcarr is correct, all the FASTQ sequences from ncbi are Phred+33.
aloliveira is offline   Reply With Quote

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