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xie186 / ViewBS

ViewBS - a powerful toolkit for visualization of high-throughput bisulfite sequencing data
GNU General Public License v3.0
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MethCoverage proportions off? #43

Closed RRebo closed 4 years ago

RRebo commented 4 years ago

Hi, I ran ViewBS on two of my BS-seq samples and for MethCoverage I get :

Sample Context Depth Percentage
NDPS122 CG 1 183.09557
NDPS122 CG 2 164.900895
NDPS122 CG 3 143.550174
NDPS122 CG 4 119.487774
NDPS122 CG 5 94.5660053
NDPS122 CG 6 70.9522451
NDPS110 CG 1 176.257886
NDPS110 CG 2 149.386972
NDPS110 CG 3 118.819988
NDPS110 CG 4 87.9548799
NDPS110 CG 5 60.4967229
NDPS110 CG 6 38.8154209

How do I have a percentage > 100? Sorry, this migt be stupid but I really don"t get it! Thanks R

xie186 commented 4 years ago

Are you using the latest version? Thanks.

RRebo commented 4 years ago

Yes, Donwloaded last week. 0.1.8?

xie186 commented 4 years ago

We'll look into this and get back to you ASAP.

xie186 commented 4 years ago

I'm not able to reproduce a result like you showed. Could you please share me the data (or a subset) to reproduce the result you showed above. Thanks. You can send the data to me via email: xie186@purdue.edu.

xie186 commented 4 years ago

Hi @RRebo,

Sorry for the late response. I checked your data. The problem was that the reference you used has large chunks of sequences with lower case bases. I have updated the code. Please use the latest version: https://github.com/xie186/ViewBS/releases

Best, Shaojun