Blobtools for symbiosis

[Sandrine3]

Hi,

I have been using blobtools to plot the diversity of symbiotic bacteria found in a plant. Everything seems to work great, the .bam file shows about 98% mapped reads depending on sample. However, when I get to plot the results, the coverage plot that is produced shows about 50% mapped reads. Why the difference?

Thank you very much for your support!
Sandrine

[Huangtianyu-caas]

Hi,

I got the same problem that the Unmapped rate is so high, and I don't know why. Do you have any update?

My best,

Tianyu

[DRL]

Hi both,

this is how coverage parsing works: https://blobtools.readme.io/docs/coverage-parsing#1-bam-files

So i would assume that the difference is due to reads that map in supplementary/secondary alignments

cheers,

dom