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No coverage or very low coverage in the Complete Genomics data

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

next-gen sequencing
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written by rse rse

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.

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written by Kevin Blighe Kevin Blighe

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

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written by rse rse

1 answer

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

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written by rse rse

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