We are trying to identify somatic mutations by comparing DNAs of normal and disease tissues. Because of the small size of the disease tissues, the DNA concentration or amount for some samples are very small. We sent 10 samples to a company to try, and 2 out of 10 (each sample generates 2 datasets) data sets failed in some of quality check. We used FastQC for QC. For these samples, we asked average coverage of 60.
The qualities that failed are:
- Per base sequence quality
- Per base GC content
- Per base sequence content
Should we increase the coverage requirement to 90 to have better quality? In general, how much coverage would give decent quality of data? We use Illumina HiSeq platform.