No coverage or very low coverage in the Complete Genomics data

Question

[rse]

Hi,

Has anyone worked on Complete Genomics data? Most of the exons in the data have no coverage or very low coverage (5-10 reads only) even though the reads are sequenced at 40X coverage. Can anyone explain why is it so?

Thanks

Regards

[Kevin Blighe]

Yes, I've worked on Complete Genomics data but I recall that the coverage was excellent genome-wide.

It's difficult to give an answer without understanding other things like:

• source and quality of template DNA
• other QC metrics such as passed filter (PF) bases, Q30 bases, alignment %, etc.

Keep in mind that the quoted depth at which samples are sequenced (here, 40x) is always the optimum value to achieve but many regions never reach this. I guess that it's like broadband Internet where they may quote 50mb/s but it only achieves 27mb/s.

[rse]

Thank you for your reply. We are pretty sure that the source and quality of DNA was good. The alignment % was around 97%. Will look into the QC meterics

Answer 1

[rse]

I’m sorry, I didn’t explain the issue properly. I’m working on CG WGS data with avg read depth of 40x. The QC metrics looks good for all parameters and the alignment rate is 97.43%. However, I had used cgaTools to convert tsv files provided by CG to BAM. When I visualize these BAM files on IGV, I see minimal coverage at all exons and major parts of introns for all genes. The trend is normally scant coverage hills at junction of intron and exon. I believe something went wrong in my conversion step. Can anyone please suggest a solution for this? Or is there any other visualization tool specific for CG data that I should be using?”

Thanks in advance