Tool like FastQC ?

[patouch74]

Hi,

I'm looking for a tool which can produce html quality report like FastQC.

I want to evaluate my data-set quality after joining paired end. So I have reads with a length range from 100 to 500 bp.
The problem with FastQC is that the boxplot quality produced has problems with the x-axis scale.

It starts with 1 2 3 4 5 6 7 8 9 then it regroups bp position such as 15-19 25-29 .. 450-499 etc. : the scale is not uniform.


I've already tested PRINSEQ but it is too slow.
So I'm looking for a tool which can deal with clear graph and as fast as FastQC.

Thanks for your help

[Michael.Ante]

Have you tried running FastQC with the "--nogroup" option?
This should prevent the scaling of the x-axis, but increases surely the computational effort.

[patouch74]

I didn't know this option but I've went to help mode and then :

--nogroup Disable grouping of bases for reads >50bp. All reports will
show data for every base in the read. WARNING: Using this
option will cause fastqc to crash and burn if you use it on
really long reads, and your plots may end up a ridiculous size.
You have been warned!

So I don't think its the right solution for me

[GenoMax]

I didn't know this option but I've went to help mode and then :

--nogroup Disable grouping of bases for reads >50bp. All reports will
show data for every base in the read. WARNING: Using this
option will cause fastqc to crash and burn if you use it on
really long reads, and your plots may end up a ridiculous size.
You have been warned!

So I don't think its the right solution for me

Have you tried it before deciding that it is not the right solution?

[wokai001]

I have made a somehow similar tool in R. Have a look at

https://r-forge.r-project.org/projects/seqtools/

You may download it from a running R session with:
install.packages("seqTools", repos="http://R-Forge.R-project.org")

Once you have collected the data, you can save your count statistics and use predefined plots or any other plotting tool in R.

Any response (or suggestion) to me on how it works would be great.

[flxlex]

You can also try preqc, part of sga: https://github.com/jts/sga/wiki/preqc