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schneebergerlab / plotsr

Tool to plot synteny and structural rearrangements between genomes
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cannot plot all the information from syri.out file #65

Closed Hemaprasanth24 closed 1 year ago

Hemaprasanth24 commented 1 year ago

hi i using syri to find synteny, inversion, translocation, duplication in a bacterial genome after getting syri.out file i have plotted it in plotsr but i can find only any one of these 4 type if synteny is present i cannot file inversion i have also checked the syri.out file it contions of both inversion as well as translocation

mnshgl0110 commented 1 year ago

Probably the rearrangements in the bacterial genomes are quite small and therefore filtered out by plotsr. You can adjust the -s parameter of plotsr to visualise smaller rearrangements.

Hemaprasanth24 commented 1 year ago

NZ_CP013910.1 1 75429 - - - - - NOTAL1 - NOTAL - NZ_CP013910.1 75430 405903 - - NZ_AP026560.1 83715 222402 SYN1 - SYN - NZ_CP013910.1 75430 75869 - - NZ_AP026560.1 83715 84154 SYNAL1 SYN1 SYNAL - NZ_CP013910.1 75463 75463 T G NZ_AP026560.1 83748 83748 SNP3 SYN1 SNP - NZ_CP013910.1 75544 75544 G A NZ_AP026560.1 83829 83829 SNP4 SYN1 SNP - NZ_CP013910.1 75549 75549 T C NZ_AP026560.1 83834 83834 SNP5 SYN1 SNP - NZ_CP013910.1 75565 75565 G C NZ_AP026560.1 83850 83850 SNP6 SYN1 SNP - NZ_CP013910.1 75567 75567 G C NZ_AP026560.1 83852 83852 SNP7 SYN1 SNP - NZ_CP013910.1 75572 75572 C G NZ_AP026560.1 83857 83857 SNP8 SYN1 SNP - NZ_CP013910.1 75574 75574 C G NZ_AP026560.1 83859 83859 SNP9 SYN1 SNP - NZ_CP013910.1 75826 75826 A G NZ_AP026560.1 84111 84111 SNP10 SYN1 SNP - NZ_CP013910.1 75827 75827 C A NZ_AP026560.1 84112 84112 SNP11 SYN1 SNP - NZ_CP013910.1 75828 75828 A G NZ_AP026560.1 84113 84113 SNP12 SYN1 SNP - NZ_CP013910.1 75837 75837 A C NZ_AP026560.1 84122 84122 SNP13 SYN1 SNP - NZ_CP013910.1 75869 405463 - - NZ_AP026560.1 84154 221962 HDR1 SYN1 HDR - NZ_CP013910.1 405464 405903 - - NZ_AP026560.1 221963 222402 SYNAL2 SYN1 SYNAL - NZ_CP013910.1 405497 405497 T G NZ_AP026560.1 221996 221996 SNP14 SYN1 SNP - NZ_CP013910.1 405578 405578 G A NZ_AP026560.1 222077 222077 SNP15 SYN1 SNP - NZ_CP013910.1 405583 405583 T C NZ_AP026560.1 222082 222082 SNP16 SYN1 SNP - NZ_CP013910.1 405599 405599 G C NZ_AP026560.1 222098 222098 SNP17 SYN1 SNP - NZ_CP013910.1 405601 405601 G C NZ_AP026560.1 222100 222100 SNP18 SYN1 SNP - NZ_CP013910.1 405606 405606 C G NZ_AP026560.1 222105 222105 SNP19 SYN1 SNP - NZ_CP013910.1 405608 405608 C G NZ_AP026560.1 222107 222107 SNP20 SYN1 SNP - NZ_CP013910.1 405860 405860 A G NZ_AP026560.1 222359 222359 SNP21 SYN1 SNP - NZ_CP013910.1 405861 405861 C A NZ_AP026560.1 222360 222360 SNP22 SYN1 SNP - NZ_CP013910.1 405862 405862 A G NZ_AP026560.1 222361 222361 SNP23 SYN1 SNP - NZ_CP013910.1 405871 405871 A C NZ_AP026560.1 222370 222370 SNP24 SYN1 SNP - NZ_CP013910.1 405904 3084300 - - - - - NOTAL2 - NOTAL - NZ_CP013910.1 3084301 3084740 - - NZ_AP026560.1 824888 825327 INV2 - INV - NZ_CP013910.1 3084301 3084740 - - NZ_AP026560.1 825327 824888 INVAL3 INV2 INVAL - NZ_CP013910.1 3084333 3084333 T G NZ_AP026560.1 825295 825295 SNP25 INV2 SNP - NZ_CP013910.1 3084342 3084342 T C NZ_AP026560.1 825286 825286 SNP26 INV2 SNP - NZ_CP013910.1 3084343 3084343 G T NZ_AP026560.1 825285 825285 SNP27 INV2 SNP - NZ_CP013910.1 3084344 3084344 T C NZ_AP026560.1 825284 825284 SNP28 INV2 SNP - NZ_CP013910.1 3084596 3084596 G C NZ_AP026560.1 825032 825032 SNP29 INV2 SNP - NZ_CP013910.1 3084598 3084598 G C NZ_AP026560.1 825030 825030 SNP30 INV2 SNP - NZ_CP013910.1 3084603 3084603 C G NZ_AP026560.1 825025 825025 SNP31 INV2 SNP - NZ_CP013910.1 3084605 3084605 C G NZ_AP026560.1 825023 825023 SNP32 INV2 SNP - NZ_CP013910.1 3084621 3084621 A G NZ_AP026560.1 825007 825007 SNP33 INV2 SNP - NZ_CP013910.1 3084626 3084626 C T NZ_AP026560.1 825002 825002 SNP34 INV2 SNP - NZ_CP013910.1 3084707 3084707 A C NZ_AP026560.1 824921 824921 SNP35 INV2 SNP - NZ_CP013910.1 3084741 3264334 - - - - - NOTAL3 - NOTAL -

this is the result i got it from syri it contain inv also but it cannot be plotted by plotsr

mnshgl0110 commented 1 year ago

did you use -s parameter?

Hemaprasanth24 commented 1 year ago

thanks for the clarifiction and i also have another problem about labelling the problem /home/hema/anaconda3/envs/py3.8/lib/python3.8/site-packages/plotsr/scripts/plotsr.py:259: UserWarning: The label 'child1' of <matplotlib.collections.LineCollection object at 0x7f9e56ec6df0> starts with ''. It is thus excluded from the legend. l1 = plt.legend(handles=chrlabels, loc='lower left', bbox_to_anchor=bbox_to_anchor, ncol=ncol, mode=None, borderaxespad=0., frameon=False, title='Genomes')

mnshgl0110 commented 1 year ago

As the original problem is resolved, I will close this issue. Please start a new issue for other problems. Also, do share the all relevant info like the command used, example input files, output generated.

Hemaprasanth24 commented 1 year ago

thank you for the reply i just correct the errror

On Thu, Aug 24, 2023 at 10:00 PM Manish Goel @.***> wrote:

did you use -s parameter?

— Reply to this email directly, view it on GitHub https://github.com/schneebergerlab/plotsr/issues/65#issuecomment-1692031781, or unsubscribe https://github.com/notifications/unsubscribe-auth/A73BTRQWFCEP35ZGP3LBQXTXW56SBANCNFSM6AAAAAA34P4R6Q . You are receiving this because you authored the thread.Message ID: @.***>