Question

Tools to compute Lorenz curve of coverage uniformity

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8.3 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 software.

Thank you in advance!

bam genome alignment • 2.8k views

ADD COMMENT • link updated 10 months ago by Ram 43k • written 8.3 years ago by igor.fobia ▴ 10

score 2 · Answer 1 · 2021-12-23

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2.3 years ago

yhoogstrate ▴ 140

Hi Igor,

I wrote a python tool to do so:

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

all best,

Youri

ADD COMMENT • link 2.3 years ago by yhoogstrate ▴ 140

Ram · Answer 2 · 2016-01-05

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8.3 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).

ADD COMMENT • link updated 21 months ago by Ram 43k • written 8.3 years ago by igor.fobia ▴ 10

score 0 · Answer 3 · 2021-12-23

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2.3 years ago

biology_inform ▴ 50

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

ADD COMMENT • link 2.3 years ago by biology_inform ▴ 50