shawnzhangyx / cvdc_scripts Goto Github PK

Hi, Thanks for your effort fot Hi-C analysis. Recently ,I want to use these scripts for our study. However ,I could not known the input format for "di_tads.10k.2M/define_boundary_by_DI_delta.r",Could you provide an test data(e-mail :[email protected]) or each column required? Thank you!

The script is below:
for sample in $(cat ../../data/hic/meta/names.txt); do
(
for chr in {1..22} X; do
echo $sample $chr
Rscript remove_pixel_wo_nearby.r ../../analysis/customLoops/tests_sample_chr/chr${chr}.${sample}.txt
Rscript colapse_pixels.r ../../analysis/customLoops/tests_sample_chr/chr${chr}.${sample}.txt.removed
done
) &
done

Could you help me how to produce the ../../analysis/customLoops/tests_sample_chr/chr${chr}.${sample}.txt file? Thank ypou very much!

Dear professor,

When I use the scripts in my human HIC, I found the signal which >200 is fewer? (THE CUTOFF 200 IN find_dynamic_boundary_DI_delta.r). Do you think this is normal ?

Dear,
Could you help me explain the following codes means. Thank you!
dat$dist = ceiling((dat$V6-dat$V2)/10000)-5