different results from fastQC and fastx toolkits

[lran2008]

Hi,

I am using fastQC to check the quality of my miRNA seq data after adaptor trimming. Then I used fastq_quality_boxplot_graph.sh from fastx toolkits to see if the results are the same as fastQC. Surprisingly, it seems that with fastq_quality_boxplot_graph.sh, the quality scores are lower (some below 30) whereas they are all above 30 using fastQC.

Could anybody tell me why there is so big difference?

There is another thread:

http://seqanswers.com/forums/showthread.php?t=20576

But in my case, I believe that all the reads have been read by fastQC or fastq_quality_boxplot_graph.sh, which can be known from their statistics.

There is indeed a very small percentage of reads which contain N. Could that be the problem? I am looking for some tools to get rid of the reads with N.

Attached are the results from fastQC and fastq_quality_boxplot_graph.sh. Thanks.

[JackieBadger]

Fastqc is smart and detected that your quality encoding. Fastq_quality_boxplot is not smart and didn't detect your encoding. As such, the later is plotting your scores on the solexa quality scale...hence values below zero.

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

[JackieBadger]

try http://edwards.sdsu.edu/cgi-bin/prinseq/prinseq.cgi

[lran2008]

Fastqc is smart and detected that your quality encoding. Fastq_quality_boxplot is not smart and didn't detect your encoding. As such, the later is plotting your scores on the solexa quality scale...hence values below zero.

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

Hi,
Thanks for your reply. The input of Fastq_quality_boxplot is the text file produced by fastx_quality_stats. I have specified -Q33 in fastx_quality_stats to get the test file. In this way, the encoding should be detected. And do you mean that results from fastQC are more reliable?

[JackieBadger]

Take a look at what the program actually does.

"FASTQ Quality Chart

$ fastq_quality_boxplot_graph.sh -h
Solexa-Quality BoxPlot plotter
Generates a solexa quality score box-plot graph "

So unless you have Solexa encoding, its no use to you.

FastqToolkit is glitchy and kind of out dated..... people have re-written many of the functions to perform better

[lran2008]

Take a look at what the program actually does.

"FASTQ Quality Chart

$ fastq_quality_boxplot_graph.sh -h
Solexa-Quality BoxPlot plotter
Generates a solexa quality score box-plot graph "

So unless you have Solexa encoding, its no use to you.

FastqToolkit is glitchy and kind of out dated..... people have re-written many of the functions to perform better

Ok, thanks.