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

[yihenghu]

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]

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