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DRL / blobtools

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
GNU General Public License v3.0
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Blobtools for symbiosis #90

Open Sandrine3 opened 4 years ago

Sandrine3 commented 4 years ago

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

nostoc_blob_M2 blobDB json bestsum order p7 span 100 noscale blobplot cumulative read_cov bam0

Huangtianyu-caas commented 3 years ago

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 commented 3 years ago

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