MiSeq fastQ quality scores

[Azazel]

I have fastQ files as output from MiSeq, 300bp directional reads. I would like to plot the distribution of quality scores for all bases (using Perl, Gnuplot or R).

I can't find definite information on how to interpret the quality string in fastQ-files coming from MiSeq.

Could anyone point me to this info? Thanks!

[kadircaner]

You might like to try FastQC : http://www.bioinformatics.babraham.a...ojects/fastqc/

[GenoMax]

I have fastQ files as output from MiSeq, 300bp directional reads. I would like to plot the distribution of quality scores for all bases (using Perl, Gnuplot or R).

I can't find definite information on how to interpret the quality string in fastQ-files coming from MiSeq.

Could anyone point me to this info? Thanks!

Information about the FASTQ format can be found here: http://en.wikipedia.org/wiki/FASTQ_format With MiSeq you are looking at quality scores in the "L" (Illumina 1.8+) format as referred to in the Wikipedia article.

[Azazel]

Information about the FASTQ format can be found here: http://en.wikipedia.org/wiki/FASTQ_format With MiSeq you are looking at quality scores in the "L" (Illumina 1.8+) format as referred to in the Wikipedia article.

@GenoMax: Thanks. I have read the Wikipedia article previously, but I find it ambiguously formulated and I don't know what the "Illumina pipeline" is. As a reader of that article, I know I using MiSeq now but it looks like this was writen only with respect to HiSeq.

I am not trying to argue, just pointing out that the Wikipedia article is a bit unclear on that point.

@kadircanir: Thanks for pointing out this program! It is excellent.

[JackieBadger]

PRINCESEQ can produce decent graphs

[JamieHeather]

You can also use the FASTX toolkit (just remember to use the -Q33 setting!) to produce quality graphs over cycle. With 300 cycles the cycle numbers will all moosh together a bit though.

[Jean]

You might like to try FastQC : http://www.bioinformatics.babraham.a...ojects/fastqc/

FastQC works well

[Buzz0r]

Hopefully, the plots generated by BaseSpace for the MiSeq output will be exportable into plots soon, that might ease some of this extra effort a bit!