Restriction fragments difference generated from HiC-Pro (digest_genome.py) and Juicer for Arima

[vikaskumar1019]

Hi,

Command used for Hic-Pro: ./digest_genome.py -r ^GATC,G^ANTC -o mm10_Arima.bed mm10.fa

I find that the restriction file generated from the output of Hic-Pro and Juicer have discrepancies

Hi-C pro result: chr1 0 3000185 HIC_chr1_1 0 + chr1 3000185 3000190 HIC_chr1_2 0 + (Difference) chr1 3000190 3000449 HIC_chr1_3 0 + chr1 3000449 3000812 HIC_chr1_4 0 + (Difference) chr1 3000812 3001047 HIC_chr1_5 0 + (Difference) chr1 3001047 3001118 HIC_chr1_6 0 + (Difference) chr1 3001118 3001460 HIC_chr1_7 0 + chr1 3001460 3001532 HIC_chr1_8 0 + chr1 3001532 3001652 HIC_chr1_9 0 + chr1 3001652 3001794 HIC_chr1_10 0 + (Difference) chr1 3001794 3003153 HIC_chr1_11 0 + chr1 3003153 3003208 HIC_chr1_12 0 + (Difference) chr1 3003208 3003262 HIC_chr1_13 0 + (Difference)

Juicer result: chr1 3000185 3000191 3000449 3000813 3001048 3001119 3001460 3001532 3001652 3001795 3003153 3003209 3003263 3003350

Can you please suggest what can be the reason for this?

Best Regards, Vikas

[nservant]

Hi Vikas, I do not see any major differences ? I have no experience with Juicer, but it seems to report only the cutting sites, while HiC-Pro provides a BED file. Of note the BED files are 0-based (meaning that the 1rst base is 0 not 1, which may explain the minor differences you have) N