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Query related to MIseq, NextSeq illumina platform

Dear Users,

I am observing Quality value represented with 'B' for the sequences obtained through these platforms.

I would like to know as per these mentioned platforms is this base considered to be of high quality or low quality.

Your inputs and suggestions will be highly appreciated.

Thank You

sequence miseq nextseq
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updated by Ram Ram • written by pinky_pinkpinky • pinky_pinkpinky

1 answer

B is typically the lowest possible quality, for old data encoded in ASCII-64/ASCII-66. You should not encounter long strings of B in modern data.

http://en.wikipedia.org/wiki/FASTQ_format

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updated by Ram Ram • written by Brian Bushnell Brian Bushnell

Illumina 1.8+ formats have switched back to Phred+33 so B is high quality potentially. I guess the OP will have to determine the original encoding to know. B is one of the unfortunate encodings that appears in every version of Illumina/Solexa Fastq encoding.

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updated by Ram Ram • written by User 59 User 59

@pinky_pinkpinky, if you are unsure about the encoding of your file run a tool like FastQC. It might be enough even to look at the first quality string of the first few reads. If you see any of these characters !"#$%&'()*+,-./0123456789: then you are Illumina 1.8. If you see KLMNOPQRSTUVWXYZ[\]^_abcdefgh` then it's old Illumina/Solexa.

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updated by Ram Ram • written by dariober dariober

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