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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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[DOC] update FAQ #344

Closed zpliu1126 closed 4 years ago

zpliu1126 commented 4 years ago

Hi~， when I want to extract chrosome loop by using juicer HiCCUPs，with the raw data from Hic-Pro。But juicer needs the data format which differ from the HiC-Pro raw data format 。 so ,I code a script multi process Python3 script，using it to change format

input file of script rawdata.allValidPairs

V300058712L1C003R0060486430/2   Gbar_A01        2514    +       Scaffold2267    21939   -       242     HIC_Gbar_A01_10 HIC_Scaffold2267_72     0       42      
V300058712L1C002R0450612435/2   Gbar_A01        16642   -       Gbar_D07        13412949        +       325     HIC_Gbar_A01_52 HIC_Gbar_D07_34935      6       38      
V300058253L1C001R0150226555/2   Gbar_A01        18197   +       Gbar_A03        105127189       +       387     HIC_Gbar_A01_58 HIC_Gbar_A03_277171     31      34      
v300043503L1C005R0160920284/2   Gbar_A01        18206   +       Gbar_A10        2363827 +       406     HIC_Gbar_A01_58 HIC_Gbar_A10_6032       31      0       
v300056214L4C005R0030513288/1   Gbar_A01        18209   +       Scaffold2267    26009   -       369     HIC_Gbar_A01_58 HIC_Scaffold2267_84     31      18

out file of script 

0 Gbar_A01 583637 0 1 Gbar_A01 584243 0
1 Gbar_A01 583655 0 1 Gbar_A01 71909032 0
1 Gbar_A01 583658 0 1 Gbar_A01 591701 0
1 Gbar_A01 583676 0 1 Gbar_A01 585746 0
1 Gbar_A01 583688 0 1 Gbar_A01 6248014 0
0 Gbar_A01 583689 0 0 Gbar_A01 588368 [0](url)

this is link of my script HicPro2juicer