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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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make_viewpoints.py: prints wrong chromosomes #180

Open rwiegan opened 6 years ago

rwiegan commented 6 years ago

Hi,

i am running the make_view point script. Genome: mm10! One track in the bedgraph file looks like this:

track type=bedGraph name='hicpro HIC_chr11_291356' description='hicpro HIC_chr11_291356' visibility=full color=200,100,0 altColor=0,100,200 priority=20 chr11 84512676 84512831 1 chr11 120220330 120221642 1 chr11 120325868 120326689 1 chr11 32416020 32416118 1 chr11 125831911 125832058 1 <--

The last fragment does not exist on chromosome 11. chromosome 11 is only 122082543 bases long. Looking for this fragment range in the restriction_map file I found it on chromosome 2.

My input files looked normal without any errors. My thought was that the make_viewpoint script is not getting the chromosome correct?

René

nservant commented 6 years ago

Really !! Any way to share with me your input files (by private mail) so that I can reproduce the issue ? Thanks

sidiropoulos commented 5 years ago

I am having the same issue, are there any updates on this?

nservant commented 5 years ago

Could you give me something to reproduce the issue ? Thanks

nadabrovitxka commented 4 years ago

Hi, This issue is still occurring for me. When I run make_viewpoints.py I always get a few fragments that are located beyond the lenght of a chromosome. Here is the .allValidPairs file.

The code used to run: make_viewpoints.py -i fastq.allValidPairs -f mm10_dpnii.bed -t target.bed -e 2000 > result.bedgraph

Genome digest file target file output make_viewpoints.py code

The output file has multiple fragments bigger than chromosome 14's length (124902244) Any insight would be really appreciated.

chr14 131628950 131630231 1 chr14 162044161 162044866 1 chr14 179133686 179133877 2 chr14 157528564 157528910 1 chr14 194338392 194338641 1 chr14 194339038 194339376 1 chr14 194339376 194339827 1 chr14 137329759 137329837 1 chr14 128346099 128347010 1 chr14 143247143 143247930 1 chr14 138953013 138953244 1 chr10 126232682 126232901 1 chr14 180419002 180419876 1 chr14 147933768 147933964 1 chr14 165769878 165770515 1 chr14 132646748 132647859 1 chr14 180798735 180798887 1 chr14 165575630 165575817 1 chr14 193066829 193067032 1 chr14 129226127 129226764 1 chr14 141257142 141257444 1 chr14 132083673 132083879 1 chr14 151723383 151723670 1 chr14 144795938 144796653 1 chr14 135203019 135203367 1 chr14 134748770 134749096 1 chr14 140799573 140801772 1 chr14 131183347 131185048 1 chr14 134008177 134009262 1 chr14 154969754 154970395 1 chr14 132346643 132346759 1 chr14 143748322 143748516 1 chr14 141446670 141446949 1 chr14 144677507 144677522 1 chr14 126286139 126286297 1 chr14 141018790 141019053 1 chr14 180568568 180569969 1 chr14 167996710 167996863 1 chr14 149525286 149525502 1 chr14 142400307 142400446 1 chr14 140316757 140317847 1 chr14 144018633 144018991 1 chr14 135346186 135346791 1 chr14 125169889 125170015 1 chr14 153565993 153566234 1 chr14 145669863 145670211 1 chr14 145670211 145670340 1 chr14 132799051 132799296 1 chr14 157253921 157254094 1 chr14 135870567 135870753 1 chr14 150743576 150745795 1 chr14 126172844 126173424 1 chr14 165168819 165168899 1 chr14 131089038 131089356 1 chr14 161254724 161255213 1 chr14 142384697 142385576 1 chr14 131398396 131399229 1 chr14 166352784 166352881 1 chr14 179300635 179300681 1 chr14 129463924 129464082 1 chr14 166951988 166953057 1 chr14 152973597 152973749 1 chr14 172641631 172642647 1 chr14 182866974 182867432 1 chr14 180020450 180020523 1 chr14 152027643 152028148 1 chr14 179491762 179492076 1 chr14 167341665 167341904 1 chr14 135988022 135988176 1 chr14 138952071 138953110 1 chr14 146426895 146427113 1 chr14 181671211 181671510 1 chr14 131614946 131615096 1 chr14 130825993 130826403 1 chr14 128430845 128431028 1 chr14 181000651 181001087 1 chr14 182321139 182321391 1 chr14 141193798 141194961 1 chr14 137993579 137994176 1 chr14 133177509 133178314 1 chr14 147683750 147683942 1 chr14 127169377 127170056 1 chr14 149870096 149870651 1 chr14 149612155 149612480 1 chr14 129896957 129897163 1 chr14 125190099 125190722 1 chr14 130517813 130518113 1 chr14 140666935 140667496 1 chr14 136684301 136684774 1 chr14 135462393 135462430 1 chr14 153915175 153915828 1 chr14 185668776 185668933 1 chr14 125422308 125423033 1 chr14 166173372 166174293 1 chr14 152956440 152956697 1 chr14 131395248 131395739 1 chr14 127285982 127286818 1 chr14 128596782 128597791 1 chr14 139014894 139015265 1 chr14 141927026 141927528 1 chr14 180143237 180143604 1 chr14 160188728 160189387 1 chr14 135548139 135548875 1 chr14 190534623 190535187 1 chr14 143008641 143008789 1 chr14 171706643 171706771 1 chr14 153339537 153340115 1 chr14 140585388 140585580 1 chr14 133619820 133620877 1 chr14 126025816 126026209 1 chr14 148810283 148810560 1 chr14 167455792 167457531 1 chr14 132718505 132718749 1 chr10 124991433 124991595 1 chr14 135613926 135614137 1 chr14 128283715 128284014 1 chr14 182828265 182828489 1 chr14 127942361 127942610 1 chr14 148858058 148858352 1 chr14 150993508 150994469 1 chr14 127218628 127219228 1 chr14 154010516 154011076 1 chr14 160369596 160369698 1 chr10 130226620 130226814 1 chr14 134197292 134197427 1 chr14 153005117 153005276 1 chr14 139077121 139077377 1 chr14 145789017 145789108 1 chr14 124996677 124997402 1 chr14 135063310 135064222 1 chr14 139023717 139024219 1 chr14 181852287 181853616 1 chr14 127496741 127497768 1 chr14 129373723 129373976 1 chr14 146931839 146932151 1 chr14 130898125 130899129 1 chr14 129817719 129818819 1 chr14 128915029 128916034 1 chr14 127896168 127896310 1 chr14 144112394 144113103 1 chr14 185317608 185318362 1 chr14 143397990 143398482 1 chr14 135971466 135971810 1 chr14 160662527 160662673 1 chr14 146670080 146670419 1 chr14 141145880 141146410 1 chr14 138201586 138202655 1 chr14 174049587 174050219 1 chr14 167199696 167200758 1 chr14 130254431 130254628 1 chr14 135188815 135188955 1 chr14 161840732 161840945 1 chr14 130212874 130213307 1 chr14 158502664 158502837 1 chr14 169957143 169958656 1 chr14 127931323 127932079 1 chr14 139228220 139228444 1 chr14 136021966 136022171 1 chr14 131646741 131647026 1 chr14 136055005 136055191 1 chr14 135734349 135734800 1 chr14 148507477 148508237 1 chr14 145408273 145408390 1 chr14 154829548 154830216 1 chr14 129356832 129357277 1 chr14 141690673 141690979 1 chr14 134550941 134552007 1 chr14 171020961 171021069 1 chr14 136804869 136805173 1 chr14 159188081 159188215 1 chr14 135786379 135786648 1 chr14 135198136 135201039 1 chr14 154756146 154756719 1 chr14 133634679 133634963 1 chr14 178619017 178619237 1 chr14 178621280 178621445 1 chr14 155826637 155827450 1 chr14 145410032 145410220 1 chr14 166358441 166359033 1 chr14 135133566 135134863 1 chr14 158440692 158441129 1 chr14 151325882 151326109 1 chr14 131606985 131607363 1 chr14 126295231 126295451 1 chr14 144193866 144194154 1 chr14 128927266 128928285 1 chr14 146622829 146623141 1 chr14 152581986 152582322 1 chr14 142685388 142685538 1 chr14 139430146 139430158 1 chr14 129319349 129320040 1 chr14 154097642 154098162 1 chr14 126538065 126539704 1 chr14 137393548 137394125 1 chr14 128571799 128572036 1 chr14 135417097 135418419 1 chr14 171524989 171525282 1 chr14 168631760 168632003 1 chr14 132429844 132430332 1 chr14 126732807 126733259 1 chr14 154901827 154902187 1 chr14 145561712 145564991 1 chr14 166693416 166694522 1 chr14 126352571 126352752 1 chr14 181240231 181241794 1 chr14 152970458 152970772 1 chr14 134049994 134051534 1 chr14 149690331 149690380 1 chr14 130565286 130565609 1 chr14 146882502 146882849 1 chr14 151028300 151028534 1 chr14 138333449 138333592 1 chr14 134487719 134489643 1 chr14 147409968 147410195 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180001596 1 chr14 174709379 174709844 1 chr14 143171995 143173230 1 chr14 125989775 125989952 1 chr14 154455840 154456070 1 chr14 151692809 151693091 1 chr14 169696061 169696671 1 chr14 135176941 135177371 1 chr14 166275747 166278982 1 chr14 130381504 130382618 1 chr14 140689389 140689459 1 chr14 148912912 148913190 1 chr14 143184952 143185680 1 chr14 156321278 156321528 1 chr14 140886608 140887263 1 chr14 184776804 184776953 1 chr14 125153281 125153509 1 chr14 151356003 151356152 1 chr14 131101683 131102993 1 chr14 140636682 140637466 1 chr14 147915557 147915704 1 chr14 153248924 153249061 1 chr14 141358493 141358889 1 chr14 145403938 145404469 1 chr14 157445209 157445412 1 chr14 149968267 149968641 1 chr14 136241912 136242309 1 chr14 165139401 165140658 1 chr14 139733175 139733535 1 chr14 181040603 181040768 1 chr14 182078241 182078497 2 chr14 153641658 153642738 1 chr14 126110969 126111406 1 chr14 125335325 125335624 1 chr14 164945696 164945921 1 chr14 132592189 132593101 1 chr14 134219195 134219379 1 chr14 146456911 146458045 1 chr14 152697866 152698542 1 chr14 153720920 153722158 1 chr14 139970768 139971222 1 chr14 154032158 154032665 1 chr14 128412233 128412596 1 chr14 145213353 145213528 1 chr14 179126298 179126355 1 chr14 127833095 127833175 1 chr14 147307440 147308032 1 chr14 157695554 157695770 1 chr14 136309856 136310081 1 chr14 138272796 138272895 1 chr14 146690974 146691308 1 chr14 144649614 144649847 1 chr14 136763690 136763766 1 chr14 142380794 142381044 1 chr14 151344414 151344932 1 chr14 129066644 129068350 1 chr14 144739317 144739446 1 chr14 141269847 141270130 1 chr14 125471728 125472057 1 chr14 139383745 139384083 1 chr14 146338849 146339047 1 chr14 148462174 148462496 1 chr14 126580832 126581116 1 chr14 126046794 126047026 1 chr14 134219342 134219554 1 chr14 147846837 147847297 1 chr14 164531759 164532020 1 chr14 178463466 178463714 1 chr14 168015843 168017550 1 chr14 144168294 144168376 1 chr14 129059849 129060050 1 chr14 150953426 150953481 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1 chr14 138382512 138382801 1 chr14 131095173 131095386 1 chr14 175714452 175714502 1 chr14 126876718 126876868 1 chr14 130857391 130857582 1 chr14 158743425 158743628 1 chr14 134310245 134310470 1 chr14 135735778 135736167 1 chr14 168490389 168490794 1 chr14 153650943 153651130 1 chr14 175603727 175603992 1 chr14 171470404 171470630 1 chr14 174863032 174863309 1 chr14 157698882 157699220 1 chr14 134537356 134537414 1 chr14 129800959 129801389 2 chr14 135819035 135819187 1 chr10 128598227 128598515 1 chr14 154115199 154115445 1 chr14 128468623 128468722 1 chr14 132035985 132036134 1 chr14 125171855 125172365 1 chr14 138735677 138735853 1 chr14 147920335 147920842 1 chr14 177119813 177120036 1 chr14 126335344 126335449 1 chr14 158921691 158922037 1 chr14 158201390 158201598 1 chr14 143935642 143936972 1 chr14 167054868 167055179 1