SOLiD 5500 Quality Control Standards

[gormleymp]

Can anyone point me to a document describing quality control standards for NGS generally and for the SOLiD 5500 specifically? I understand the BAMStats module offers quality control metrics but I need documentation to interpret them.

The current project is RNA-seq. I have seen references for third party tools like RNA-SeQC and RSeQC. Are these applicable to SOLiD data or tuned for Illumina? These tools describe a number of metrics but they do not describe how these metrics should be interpreted (i.e. what values indicate quality data? what values indicate questionable data).

Thanks,
Mike

[yl01]

BAMstats is a module of LifeScope. You can try to find documentation of it in LifeScope manual. Another QC tool suggested by Life Biotechnologies people is fastQC. It runs on LifeScope produced BAM files.

[jimmyinfrance]

After going through the updated library prep protocol for wildfire we noted the "conversion" step, with a series of additional PCR cycles (6x). Has anyone had experience with the consequence of these additional cycles? PCR duplicate rate for example?