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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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Valid Pair format explanation #426

Closed shanwai1234 closed 3 years ago

shanwai1234 commented 3 years ago

Hello,

I have used HiCPro to generate valid pairs using allele-specific mode as below, however, I want to use these valid pairs to do some further analysis, but I can not find the meaning of the format in the manual and am not sure about the format meaning of this valid pair data. Could you give me some ideas? Thank you so much!

E00513:63:H2V37CCX2:8:2116:16498:70574  Chr1     1767    -       Chr1      8888    +       182     HIC_Chr1_8        HIC_Chr1_33       8       42
      0-0
nservant commented 3 years ago

Hi

read_name / chr_A / start_A / strand_A / chr_B / start_B / strand_B / insert size / fragment_name_A / fragment_name_B / mapQ_A / mapQ_B / allele-specific info

shanwai1234 commented 3 years ago

Thank you @nservant !

Gemma-Zhang-326 commented 2 years ago

Hi

read_name / chr_A / start_A / strand_A / chr_B / start_B / strand_B / insert size / fragment_name_A / fragment_name_B / mapQ_A / mapQ_B / allele-specific info

Hi I wonder what this insert size means? And whether I can use this criteria to sample interactions which ranges from 5Kb to 2Mb from validPairs files. Many thanks.

YichaoOU commented 2 years ago

@nservant, why there are reads with the same start but belong to different fragment name?

NB551526:131:HC7YWAFX2:2:21112:13180:17535      ABC   861     +       ABC   3640    +       328     HIC_ABC_10    HIC_ABC_22    42      40      
NB551526:131:HC7YWAFX2:1:11111:2623:11403       ABC   861     -       ABC   3762    +       213     HIC_ABC_8     HIC_ABC_22    3       42