Query related to MIseq, NextSeq illumina platform

Question

[pinky_pinkpinky]

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

Answer 1

[Brian Bushnell]

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

[User 59]

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.

[dariober]

@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.