Tools to compute Lorenz curve of coverage uniformity
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Entering edit mode
6.4 years ago
igor.fobia ▴ 10

I would like to compute a Lorenz curve of per-base coverage depth for a BAM file on a certain BED file. I can find a way to do it by myself, but it would be great if you could point me to some existing softwares.

Thank you in advance!

tools alignment genome bam • 2.1k views
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Entering edit mode
5 months ago
yhoogstrate ▴ 110

Hi Igor,

I wrote a python tool to do so:

https://github.com/yhoogstrate/bam-lorenz-coverage

all best,

Youri

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6.4 years ago
igor.fobia ▴ 10

htSeqTools (with giniCoverage function) seems the only ready-to-use tool I have found for this task. However, it does not allow to restrict the analysis on a specific region (for example, by using a BED file).

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5 months ago
edus_bioinfo ▴ 10

https://blog.addgene.org/ngs-quality-control-for-pooled-libraries you can check the comments there is a comment by will including a link which is plsa.py

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