Meaning of coverage depth different between platforms?

[LouiseT]

Hi there
I am comparing exome seq data from 3 platforms; Solid4, Solid5500 and HiSeq(Illumina).
I have set the min. depth to 10 but I am wondering if this present the same meaning across all platforms.
Because of different read lenghts etc, could it be that depth 10 in platform A gives the same reliability in variant calling as depth 8 in platform B?
Which factors would you consider when comparing the meaning of depth between platforms?

Thanks,
Louise

[Torst]

Hello from Melbourne.

No, read depth is independent of read length.

Depth will depend on the genome size of the organism you sequenced however. It's the average number of reads that include a specific base in the genome.

Another thing to consider is the QUALITY of the bases in the reads. More depth won't be as beneficial if the reads have lower quality (ie. more chance of error).