About the "-rw" parameter. Could I get a new regional AQI score using intermediate or final results?

JiaoLaboratory / CRAQ

Identification of errors in draft genome assemblies with single-base pair resolution for quality assessment and improvement

https://doi.org/10.1038/s41467-023-42336-w

MIT License

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About the "-rw" parameter. Could I get a new regional AQI score using intermediate or final results? #3

Open yihenghu opened 11 months ago

yihenghu commented 11 months ago

Is there a way by adjusting the window size(-rw) for obtaining regional AQI scores and plot it from intermediate or final files? instead of rerunning CRAQ to get a new out_regional.AQI.bdg?

JiaoLaboratory commented 11 months ago

Thanks for your good suggestion! Sure, to achieve this you could follow:

step1: Get user-specified regional(i.e. window=10000) AQI score.

cat locER_out/out_final.CRE.bed strER_out/out_final.CSE.bed >CRE_CSE.bed perl CRAQ/src/regional_AQI.pl ../seq.size 10000 10000 CRE_CSE.bed >w10k_AQI.out

step2: plot AQI score.

python CRAQ/src/CRAQcircos.py --genome_size ../seq.size --genome_error_loc CRE_CSE.bed --genome_score w10k_AQI.out --output w10k_AQI.out.pdf