SOLiD QV plot

[av_d]

How to plot the QV distribution of SOLiD data ? Is there any tool available?

[ECO]

Did you search? Moving to SOLiD forum.

[KevinLam]

have you tried fastqc?

http://hts.rutgers.edu/filter/ is also useful in assessing QV distribution

[golharam]

Is anyone using FastQC on 5500 data? Apparently I need to convert the .csfasta/.qual files first to .fastq. There are several csfasta2fastq tools out there, but I can't get a single one to work on my data. My data is divided in 4 files, F3 csfasta/qual and F5_RNA csfasta/qual. Why, I don't know (yet). The versions of csfasta2qual I found don't like this very much. Or is there a different QV analysis tool I should be using?

[rivabros]

hi golharam,
use the SOLiD2std.pl to change the csfasta and qual files to standard fastq files.
then run fastqc to view boxplots of quality data, etc..
II think the qual file must be <prefix>.qual (not .QV)

cheers
maximo

[colindaven]

golharam - you can try prinseq as well.

http://edwards.sdsu.edu/cgi-bin/prinseq/prinseq.cgi?home=1

The initial results are ok but the real beauty is in the graph output file, which can also be produced online.

Another way to use FastQC is by first aligning and then reading the BAM files.