QC metrics for RNAseq data from 5500xl

[fatakias]

Dear all,

I need to generate the QC metrics of a dataset generated from LifeTechnology's SOLiD sequencer (SOLiD4 as well as the 5500xl). The output file format from the sequencer is xsq file format (eXtensible File format). Can some one please help suggest a way out.

FastQC has been a very critical tool for such QC metrics but uploads files in fastq format.
So how can I convert an xsq file to a fastq format?
or
How can I generate QC metrics using xsq files from the sequencer?

One way out is to use convert xsq file to csfasta and qual files, then use "solid2fastq" function from Bfast to convert it to fastq file. It is a two step process. Is this the only unique and elegant solution?
Hope the experts can help suggest.
Thanks in advance.

[simonandrews]

In theory we could support this as an input format in FastQC since there is documentation for the file format, but it's not something I'm likely to get around to soon since this isn't something my group is ever likely to use. If LifeTechnology have a java library to read this format (similar to picard for BAM/SAM) then it would be trivial to add support for it, but as their tools download requires acceptance of a EULA then I can't easily check, and couldn't integrate it with FastQC anyway.

If anyone is working on an open library for this I'd be happy to collaborate to help to get it into a usable state.

[Jorge Amigo]

a [rather slow] way of circumvent this is to use XSQtools to convert xsq files into fastq format, and then analyze them in FastQC. it's not optimal, although I haven't found any other way to get it to work.

[colindaven]

I convert XSQ to csfasta, align, then read the BAM into FastQC. Also not elegant but it works.
I'm not sure I yet properly trust .csfasta and .qual to fastq conversion.

[Jorge Amigo]

my solution is if you want/need to get FastQC metrics BEFORE aligning, in order to evaluate if your experiment has performed well and if you want to spend computing time further analyzing it. if you don't mind using FastQC AFTER aligning, you could use LifeTech's LifeScope for the alignment (it logically deals with XSQ format natively) without any format conversion in the middle, and then get FastQC to work with LifeScope's BAM files.