ERROR: no inter-ligation PETs detected for eps 5000 minPts 50,can't model the distance cutoff,continue anyway

YaqiangCao / cLoops

Accurate and flexible loops calling tool for 3D genomic data.

https://yaqiangcao.github.io/cLoops/

MIT License

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ERROR: no inter-ligation PETs detected for eps 5000 minPts 50,can't model the distance cutoff,continue anyway #24

Closed ysora closed 4 years ago

ysora commented 4 years ago

I am trying to run cLoops with a public data (Vian et al., 2018) but it gives error as below:

cooler dump --join GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30.mcool::resolutions/5000 -o GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.bedpe

cLoops -f GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.bedpe -o GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.cLoops -j -m 3

2020-11-12 15:19:44,166 INFO Command line: cLoops -f GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.bedpe -o GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.cLoops -m 3 -eps 0 -minPts 0 -p 1 -w False -j True -s False -c -hic False -cut 0 -plot False -max_cut False 2020-11-12 15:19:44,166 INFO mode:3 eps:[5000, 7500, 10000] minPts:[50, 40, 30, 20] hic:1
2020-11-12 15:19:44,178 INFO Parsing PETs from GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.bedpe, requiring initial distance cutoff > 0 632800000 PETs processed from GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.bedpe() 2020-11-12 18:27:59,059 INFO Totaly 632884895 PETs from GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.bedpe, in which 0 cis PETs 2020-11-12 18:27:59,180 INFO ERROR: no inter-ligation PETs detected for eps 5000 minPts 50,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,180 INFO ERROR: no inter-ligation PETs detected for eps 5000 minPts 40,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,181 INFO ERROR: no inter-ligation PETs detected for eps 5000 minPts 30,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,181 INFO ERROR: no inter-ligation PETs detected for eps 5000 minPts 20,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,181 INFO ERROR: no inter-ligation PETs detected for eps 7500 minPts 50,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,181 INFO ERROR: no inter-ligation PETs detected for eps 7500 minPts 40,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,181 INFO ERROR: no inter-ligation PETs detected for eps 7500 minPts 30,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,181 INFO ERROR: no inter-ligation PETs detected for eps 7500 minPts 20,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,182 INFO ERROR: no inter-ligation PETs detected for eps 10000 minPts 50,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,182 INFO ERROR: no inter-ligation PETs detected for eps 10000 minPts 40,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,183 INFO ERROR: no inter-ligation PETs detected for eps 10000 minPts 30,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,183 INFO ERROR: no inter-ligation PETs detected for eps 10000 minPts 20,can't model the distance cutoff,continue anyway Traceback (most recent call last): File "/mnt/data0/apps/anaconda/Anaconda2-5.2/bin/cLoops", line 11, in load_entry_point('cLoops==0.93', 'console_scripts', 'cLoops')() File "build/bdist.linux-x86_64/egg/cLoops/pipe.py", line 349, in main File "build/bdist.linux-x86_64/egg/cLoops/pipe.py", line 280, in pipe File "/mnt/data0/apps/anaconda/Anaconda2-5.2/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 2618, in amin initial=initial) File "/mnt/data0/apps/anaconda/Anaconda2-5.2/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction return ufunc.reduce(obj, axis, dtype, out, **passkwargs) ValueError: zero-size array to reduction operation minimum which has no identity

Please let me know if there is something that I missed. Thanks.

YaqiangCao commented 4 years ago

Dear User, Could you please show me first several lines of your BEDPE file? According to the log information, seems there is no intra-chromosomal PETs in your file. Best, Yaqiang

On Thu, Nov 12, 2020 at 6:47 PM Sora Yoon (윤소라) notifications@github.com wrote:

I am trying to run cLoops with a public data (Vian et al., 2018) but it gives error as below:

cooler dump --join GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30.mcool::resolutions/5000 -o GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.bedpe

cLoops -f GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.bedpe -o GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.cLoops -j -m 3

2020-11-12 15:19:44,166 INFO Command line: cLoops -f GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.bedpe -o GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.cLoops -m 3 -eps 0 -minPts 0 -p 1 -w False -j True -s False -c -hic False -cut 0 -plot False -max_cut False 2020-11-12 15:19:44,166 INFO mode:3 eps:[5000, 7500, 10000] minPts:[50, 40, 30, 20] hic:1 2020-11-12 15:19:44,178 INFO Parsing PETs from GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.bedpe, requiring initial distance cutoff > 0 632800000 PETs processed from GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.bedpe() 2020-11-12 18:27:59,059 INFO Totaly 632884895 PETs from GSE82144_Kieffer-Kwon-2017-activated_B_cells_72_hours_WT_30_res5kb.bedpe, in which 0 cis PETs 2020-11-12 18:27:59,180 INFO ERROR: no inter-ligation PETs detected for eps 5000 minPts 50,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,180 INFO ERROR: no inter-ligation PETs detected for eps 5000 minPts 40,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,181 INFO ERROR: no inter-ligation PETs detected for eps 5000 minPts 30,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,181 INFO ERROR: no inter-ligation PETs detected for eps 5000 minPts 20,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,181 INFO ERROR: no inter-ligation PETs detected for eps 7500 minPts 50,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,181 INFO ERROR: no inter-ligation PETs detected for eps 7500 minPts 40,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,181 INFO ERROR: no inter-ligation PETs detected for eps 7500 minPts 30,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,181 INFO ERROR: no inter-ligation PETs detected for eps 7500 minPts 20,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,182 INFO ERROR: no inter-ligation PETs detected for eps 10000 minPts 50,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,182 INFO ERROR: no inter-ligation PETs detected for eps 10000 minPts 40,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,183 INFO ERROR: no inter-ligation PETs detected for eps 10000 minPts 30,can't model the distance cutoff,continue anyway 2020-11-12 18:27:59,183 INFO ERROR: no inter-ligation PETs detected for eps 10000 minPts 20,can't model the distance cutoff,continue anyway Traceback (most recent call last): File "/mnt/data0/apps/anaconda/Anaconda2-5.2/bin/cLoops", line 11, in load_entry_point('cLoops==0.93', 'console_scripts', 'cLoops')() File "build/bdist.linux-x86_64/egg/cLoops/pipe.py", line 349, in main File "build/bdist.linux-x86_64/egg/cLoops/pipe.py", line 280, in pipe File "/mnt/data0/apps/anaconda/Anaconda2-5.2/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 2618, in amin initial=initial) File "/mnt/data0/apps/anaconda/Anaconda2-5.2/lib/python2.7/site-packages/numpy/core/fromnumeric.py", line 86, in _wrapreduction return ufunc.reduce(obj, axis, dtype, out, **passkwargs) ValueError: zero-size array to reduction operation minimum which has no identity

Please let me know if there is something that I missed. Thanks.

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ysora commented 4 years ago

It looks like this:

chr1 2995000 3000000 chr2 30065000 30070000 1 chr1 3000000 3005000 chr1 3000000 3005000 363 chr1 3000000 3005000 chr1 3005000 3010000 26 chr1 3000000 3005000 chr1 3010000 3015000 50 chr1 3000000 3005000 chr1 3015000 3020000 23 chr1 3000000 3005000 chr1 3020000 3025000 27 chr1 3000000 3005000 chr1 3025000 3030000 11 chr1 3000000 3005000 chr1 3030000 3035000 4 chr1 3000000 3005000 chr1 3035000 3040000 14 chr1 3000000 3005000 chr1 3040000 3045000 9 chr1 3000000 3005000 chr1 3045000 3050000 3 chr1 3000000 3005000 chr1 3050000 3055000 7 chr1 3000000 3005000 chr1 3055000 3060000 9 chr1 3000000 3005000 chr1 3060000 3065000 5 chr1 3000000 3005000 chr1 3065000 3070000 2 chr1 3000000 3005000 chr1 3070000 3075000 4 chr1 3000000 3005000 chr1 3075000 3080000 3 chr1 3000000 3005000 chr1 3080000 3085000 4 chr1 3000000 3005000 chr1 3085000 3090000 3 chr1 3000000 3005000 chr1 3090000 3095000 2 chr1 3000000 3005000 chr1 3095000 3100000 4 chr1 3000000 3005000 chr1 3100000 3105000 5 chr1 3000000 3005000 chr1 3105000 3110000 4 chr1 3000000 3005000 chr1 3110000 3115000 5 chr1 3000000 3005000 chr1 3115000 3120000 3 chr1 3000000 3005000 chr1 3120000 3125000 2 chr1 3000000 3005000 chr1 3125000 3130000 1 chr1 3000000 3005000 chr1 3130000 3135000 2 chr1 3000000 3005000 chr1 3135000 3140000 4 chr1 3000000 3005000 chr1 3140000 3145000 1 chr1 3000000 3005000 chr1 3145000 3150000 1 chr1 3000000 3005000 chr1 3150000 3155000 2 chr1 3000000 3005000 chr1 3155000 3160000 2 chr1 3000000 3005000 chr1 3160000 3165000 3 chr1 3000000 3005000 chr1 3165000 3170000 1 chr1 3000000 3005000 chr1 3170000 3175000 2 chr1 3000000 3005000 chr1 3175000 3180000 1 chr1 3000000 3005000 chr1 3185000 3190000 3 chr1 3000000 3005000 chr1 3190000 3195000 1 chr1 3000000 3005000 chr1 3195000 3200000 1 chr1 3000000 3005000 chr1 3200000 3205000 5 chr1 3000000 3005000 chr1 3205000 3210000 3 chr1 3000000 3005000 chr1 3210000 3215000 3 chr1 3000000 3005000 chr1 3215000 3220000 6 chr1 3000000 3005000 chr1 3220000 3225000 2 chr1 3000000 3005000 chr1 3225000 3230000 3 chr1 3000000 3005000 chr1 3235000 3240000 2 chr1 3000000 3005000 chr1 3240000 3245000 6 chr1 3000000 3005000 chr1 3245000 3250000 3 chr1 3000000 3005000 chr1 3250000 3255000 2 chr1 3000000 3005000 chr1 3255000 3260000 2 chr1 3000000 3005000 chr1 3260000 3265000 3 chr1 3000000 3005000 chr1 3270000 3275000 1 chr1 3000000 3005000 chr1 3280000 3285000 4 chr1 3000000 3005000 chr1 3285000 3290000 3 chr1 3000000 3005000 chr1 3295000 3300000 2 chr1 3000000 3005000 chr1 3300000 3305000 3 chr1 3000000 3005000 chr1 3310000 3315000 3 chr1 3000000 3005000 chr1 3315000 3320000 1 chr1 3000000 3005000 chr1 3320000 3325000 6 chr1 3000000 3005000 chr1 3325000 3330000 3 chr1 3000000 3005000 chr1 3330000 3335000 2 chr1 3000000 3005000 chr1 3340000 3345000 1 chr1 3000000 3005000 chr1 3345000 3350000 1 chr1 3000000 3005000 chr1 3350000 3355000 1 chr1 3000000 3005000 chr1 3355000 3360000 2 chr1 3000000 3005000 chr1 3360000 3365000 1 chr1 3000000 3005000 chr1 3365000 3370000 1 chr1 3000000 3005000 chr1 3375000 3380000 1 chr1 3000000 3005000 chr1 3380000 3385000 3

ysora commented 4 years ago

Can it be the problem of data resolution?? Here, I used 5kb data. Do you think it is too sparse to use?

YaqiangCao commented 4 years ago

Hi Sora, cLoops use raw PETs to call loops. I can not call if it is too sparse. Additionally, each item in the line is separated by \t or space? For cLoops, \t is used to parse each line. Best, Yaqiang

On Thu, Nov 12, 2020 at 6:55 PM Sora Yoon (윤소라) notifications@github.com wrote:

Can it be the problem of data resolution?? Here, I used 5kb data. Do you think it is too sparse to use?

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ysora commented 4 years ago

Yes, I will try with 10kb resolution data. The data is tab-delimited. Thanks.

YaqiangCao commented 4 years ago

Could you please send me one chromosome data for test? For example chr21 of human or chr19 of mouse.

On Thu, Nov 12, 2020 at 7:15 PM Sora Yoon (윤소라) notifications@github.com wrote:

Yes, I will try with 10kb resolution data. The data is tab-delimited. Thanks.

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ysora commented 4 years ago

You mean the .bedpe file?? Sure, I will do that.

YaqiangCao commented 4 years ago

Yes, the .bedpe file.

On Thu, Nov 12, 2020 at 7:44 PM Sora Yoon (윤소라) notifications@github.com wrote:

You mean the .bedpe file?? Sure, I will do that.

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ysora commented 4 years ago

Yoon, Sora has shared a OneDrive for Business file with you. To view it, click the link below. https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ [https://r1.res.office365.com/owa/prem/images/dc-zip_20.png]https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ Vian_ab_72h_res10kb_chr19.ziphttps://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ

I also had a same error with 10kb resolution data. Here, I send you the bedpe file of chr19. Thanks,

Sora

From: YaqiangCao notifications@github.com Sent: Thursday, November 12, 2020 7:49 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author author@noreply.github.com Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

Yes, the .bedpe file.

On Thu, Nov 12, 2020 at 7:44 PM Sora Yoon (윤소라) notifications@github.com wrote:

You mean the .bedpe file?? Sure, I will do that.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/YaqiangCao/cLoops/issues/24#issuecomment-726431422, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAOPQKNDJ5OYCHM5NWOSB7LSPR6OZANCNFSM4TT5OWAQ .

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YaqiangCao commented 4 years ago

HI Sora, I have problems to access the files, seems only Penn can access. Best, Yaqiang

On Fri, Nov 13, 2020 at 1:05 PM Sora Yoon (윤소라) notifications@github.com wrote:

Yoon, Sora has shared a OneDrive for Business file with you. To view it, click the link below. < https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

[https://r1.res.office365.com/owa/prem/images/dc-zip_20.png]< https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

Vian_ab_72h_res10kb_chr19.zip< https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

I also had a same error with 10kb resolution data. Here, I send you the bedpe file of chr19. Thanks,

Sora

From: YaqiangCao notifications@github.com Sent: Thursday, November 12, 2020 7:49 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

Yes, the .bedpe file.

On Thu, Nov 12, 2020 at 7:44 PM Sora Yoon (윤소라) notifications@github.com

wrote:

You mean the .bedpe file?? Sure, I will do that.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/YaqiangCao/cLoops/issues/24#issuecomment-726431422,

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.

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ysora commented 4 years ago

I'd like to share it through google drive. Could you send me your email? Thanks.

Sora

From: YaqiangCao notifications@github.com Sent: Friday, November 13, 2020 3:32 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author author@noreply.github.com Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

HI Sora, I have problems to access the files, seems only Penn can access. Best, Yaqiang

On Fri, Nov 13, 2020 at 1:05 PM Sora Yoon (윤소라) notifications@github.com wrote:

Yoon, Sora has shared a OneDrive for Business file with you. To view it, click the link below. < https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

[https://r1.res.office365.com/owa/prem/images/dc-zip_20.png]< https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

Vian_ab_72h_res10kb_chr19.zip< https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

I also had a same error with 10kb resolution data. Here, I send you the bedpe file of chr19. Thanks,

Sora

From: YaqiangCao notifications@github.com Sent: Thursday, November 12, 2020 7:49 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

Yes, the .bedpe file.

On Thu, Nov 12, 2020 at 7:44 PM Sora Yoon (윤소라) notifications@github.com

wrote:

You mean the .bedpe file?? Sure, I will do that.

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.

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YaqiangCao commented 4 years ago

my email is caoyaqiang0410@gmail.com

On Fri, Nov 13, 2020 at 3:53 PM Sora Yoon (윤소라) notifications@github.com wrote:

I'd like to share it through google drive. Could you send me your email? Thanks.

Sora

From: YaqiangCao notifications@github.com Sent: Friday, November 13, 2020 3:32 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

HI Sora, I have problems to access the files, seems only Penn can access. Best, Yaqiang

On Fri, Nov 13, 2020 at 1:05 PM Sora Yoon (윤소라) notifications@github.com

wrote:

Yoon, Sora has shared a OneDrive for Business file with you. To view it, click the link below. <

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

[https://r1.res.office365.com/owa/prem/images/dc-zip_20.png]<

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

Vian_ab_72h_res10kb_chr19.zip<

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

I also had a same error with 10kb resolution data. Here, I send you the bedpe file of chr19. Thanks,

Sora

From: YaqiangCao notifications@github.com Sent: Thursday, November 12, 2020 7:49 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

Yes, the .bedpe file.

On Thu, Nov 12, 2020 at 7:44 PM Sora Yoon (윤소라) < notifications@github.com>

wrote:

You mean the .bedpe file?? Sure, I will do that.

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ysora commented 4 years ago

Please check the email. Thanks

Sora

From: YaqiangCao notifications@github.com Sent: Friday, November 13, 2020 4:30 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author author@noreply.github.com Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

my email is caoyaqiang0410@gmail.com

On Fri, Nov 13, 2020 at 3:53 PM Sora Yoon (윤소라) notifications@github.com wrote:

I'd like to share it through google drive. Could you send me your email? Thanks.

Sora

From: YaqiangCao notifications@github.com Sent: Friday, November 13, 2020 3:32 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

HI Sora, I have problems to access the files, seems only Penn can access. Best, Yaqiang

On Fri, Nov 13, 2020 at 1:05 PM Sora Yoon (윤소라) notifications@github.com

wrote:

Yoon, Sora has shared a OneDrive for Business file with you. To view it, click the link below. <

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

[https://r1.res.office365.com/owa/prem/images/dc-zip_20.png]<

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

Vian_ab_72h_res10kb_chr19.zip<

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

I also had a same error with 10kb resolution data. Here, I send you the bedpe file of chr19. Thanks,

Sora

From: YaqiangCao notifications@github.com Sent: Thursday, November 12, 2020 7:49 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

Yes, the .bedpe file.

On Thu, Nov 12, 2020 at 7:44 PM Sora Yoon (윤소라) < notifications@github.com>

wrote:

You mean the .bedpe file?? Sure, I will do that.

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YaqiangCao commented 4 years ago

Hi Sara, In your bedpe file, only 7 columns, meanwhile following are required for cLoops. (https://github.com/YaqiangCao/cLoops) . [image: image.png] Additionally, cLoops uses raw PETs to find loops. Meanwhile in your data, it seems the bins and PETs in it, by default each line from BEDPE file cLoops will consider it as a PET, not multiple. If you use HICPro process the fastq files, you can use https://github.com/YaqiangCao/cLoops/blob/master/scripts/hicpropairs2bedpe to convert to cLoops input BEDPE file. With your BEDPE data, I am afraid I can not find loops. Could you please show me some screenshot of your chr19 with Juicebox or other tools? If you can observe loops visually, cLoops should detect them. Best, Yaqiang

On Fri, Nov 13, 2020 at 4:33 PM Sora Yoon (윤소라) notifications@github.com wrote:

Please check the email. Thanks

Sora

From: YaqiangCao notifications@github.com Sent: Friday, November 13, 2020 4:30 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

my email is caoyaqiang0410@gmail.com

On Fri, Nov 13, 2020 at 3:53 PM Sora Yoon (윤소라) notifications@github.com

wrote:

I'd like to share it through google drive. Could you send me your email? Thanks.

Sora

From: YaqiangCao notifications@github.com Sent: Friday, November 13, 2020 3:32 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

HI Sora, I have problems to access the files, seems only Penn can access. Best, Yaqiang

On Fri, Nov 13, 2020 at 1:05 PM Sora Yoon (윤소라) < notifications@github.com>

wrote:

Yoon, Sora has shared a OneDrive for Business file with you. To view it, click the link below. <

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

[https://r1.res.office365.com/owa/prem/images/dc-zip_20.png]<

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

Vian_ab_72h_res10kb_chr19.zip<

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

I also had a same error with 10kb resolution data. Here, I send you the bedpe file of chr19. Thanks,

Sora

From: YaqiangCao notifications@github.com Sent: Thursday, November 12, 2020 7:49 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

Yes, the .bedpe file.

On Thu, Nov 12, 2020 at 7:44 PM Sora Yoon (윤소라) < notifications@github.com>

wrote:

You mean the .bedpe file?? Sure, I will do that.

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ysora commented 4 years ago

Thanks for fast responsee. I don't have HiCPro result but only have .cool or .hic file. Can I generate appropriate input format from those file types? Thanks.

Sora

From: YaqiangCao notifications@github.com Sent: Friday, November 13, 2020 5:10 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author author@noreply.github.com Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

On Fri, Nov 13, 2020 at 4:33 PM Sora Yoon (윤소라) notifications@github.com wrote:

Please check the email. Thanks

Sora

From: YaqiangCao notifications@github.com Sent: Friday, November 13, 2020 4:30 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

my email is caoyaqiang0410@gmail.com

On Fri, Nov 13, 2020 at 3:53 PM Sora Yoon (윤소라) notifications@github.com

wrote:

I'd like to share it through google drive. Could you send me your email? Thanks.

Sora

From: YaqiangCao notifications@github.com Sent: Friday, November 13, 2020 3:32 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

HI Sora, I have problems to access the files, seems only Penn can access. Best, Yaqiang

On Fri, Nov 13, 2020 at 1:05 PM Sora Yoon (윤소라) < notifications@github.com>

wrote:

Yoon, Sora has shared a OneDrive for Business file with you. To view it, click the link below. <

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

[https://r1.res.office365.com/owa/prem/images/dc-zip_20.png]<

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

Vian_ab_72h_res10kb_chr19.zip<

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

I also had a same error with 10kb resolution data. Here, I send you the bedpe file of chr19. Thanks,

Sora

From: YaqiangCao notifications@github.com Sent: Thursday, November 12, 2020 7:49 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

Yes, the .bedpe file.

On Thu, Nov 12, 2020 at 7:44 PM Sora Yoon (윤소라) < notifications@github.com>

wrote:

You mean the .bedpe file?? Sure, I will do that.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/YaqiangCao/cLoops/issues/24#issuecomment-726431422>,

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ysora commented 4 years ago

[cid:05833d65-923d-4f8f-85a8-ad9b950a1eb1]

Yes, chr19 has clear loops like this.

[cid:816e1ffb-ace3-4135-9f4e-7cb9f98c2b37] This is coordinate information. Thanks.

Sora

On Fri, Nov 13, 2020 at 4:33 PM Sora Yoon (윤소라) notifications@github.com wrote:

Please check the email. Thanks

Sora

From: YaqiangCao notifications@github.com Sent: Friday, November 13, 2020 4:30 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

my email is caoyaqiang0410@gmail.com

On Fri, Nov 13, 2020 at 3:53 PM Sora Yoon (윤소라) notifications@github.com

wrote:

I'd like to share it through google drive. Could you send me your email? Thanks.

Sora

From: YaqiangCao notifications@github.com Sent: Friday, November 13, 2020 3:32 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

HI Sora, I have problems to access the files, seems only Penn can access. Best, Yaqiang

On Fri, Nov 13, 2020 at 1:05 PM Sora Yoon (윤소라) < notifications@github.com>

wrote:

Yoon, Sora has shared a OneDrive for Business file with you. To view it, click the link below. <

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

[https://r1.res.office365.com/owa/prem/images/dc-zip_20.png]<

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

Vian_ab_72h_res10kb_chr19.zip<

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

I also had a same error with 10kb resolution data. Here, I send you the bedpe file of chr19. Thanks,

Sora

From: YaqiangCao notifications@github.com Sent: Thursday, November 12, 2020 7:49 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

Yes, the .bedpe file.

On Thu, Nov 12, 2020 at 7:44 PM Sora Yoon (윤소라) < notifications@github.com>

wrote:

You mean the .bedpe file?? Sure, I will do that.

— You are receiving this because you commented. Reply to this email directly, view it on GitHub < https://github.com/YaqiangCao/cLoops/issues/24#issuecomment-726431422>,

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YaqiangCao commented 4 years ago

Hi Sora, I am not sure if Juicer or HiCExplor can export PETs level all data. One possible solution I guess is export with smallest resolution as 1KB, for one record chr1 xs xe chr2 ye ys 3, in the region you random generate 3 BEDPE records. It will affect the boundaries, however, I think will call loops. Better to start with raw PETs. Or you can just try HiCCUPS from Juicer to call loops with the .hic files. Best, Yaqiang

On Fri, Nov 13, 2020 at 5:22 PM Sora Yoon (윤소라) notifications@github.com wrote:

Thanks for fast responsee. I don't have HiCPro result but only have .cool or .hic file. Can I generate appropriate input format from those file types? Thanks.

Sora

From: YaqiangCao notifications@github.com Sent: Friday, November 13, 2020 5:10 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

Hi Sara, In your bedpe file, only 7 columns, meanwhile following are required for cLoops. (https://github.com/YaqiangCao/cLoops) . [image: image.png] Additionally, cLoops uses raw PETs to find loops. Meanwhile in your data, it seems the bins and PETs in it, by default each line from BEDPE file cLoops will consider it as a PET, not multiple. If you use HICPro process the fastq files, you can use https://github.com/YaqiangCao/cLoops/blob/master/scripts/hicpropairs2bedpe to convert to cLoops input BEDPE file. With your BEDPE data, I am afraid I can not find loops. Could you please show me some screenshot of your chr19 with Juicebox or other tools? If you can observe loops visually, cLoops should detect them. Best, Yaqiang

On Fri, Nov 13, 2020 at 4:33 PM Sora Yoon (윤소라) notifications@github.com

wrote:

Please check the email. Thanks

Sora

From: YaqiangCao notifications@github.com Sent: Friday, November 13, 2020 4:30 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

my email is caoyaqiang0410@gmail.com

On Fri, Nov 13, 2020 at 3:53 PM Sora Yoon (윤소라) < notifications@github.com>

wrote:

I'd like to share it through google drive. Could you send me your email? Thanks.

Sora

From: YaqiangCao notifications@github.com Sent: Friday, November 13, 2020 3:32 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

HI Sora, I have problems to access the files, seems only Penn can access. Best, Yaqiang

On Fri, Nov 13, 2020 at 1:05 PM Sora Yoon (윤소라) < notifications@github.com>

wrote:

Yoon, Sora has shared a OneDrive for Business file with you. To view it, click the link below. <

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

[https://r1.res.office365.com/owa/prem/images/dc-zip_20.png]<

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

Vian_ab_72h_res10kb_chr19.zip<

https://pennmedicine-my.sharepoint.com/:u:/g/personal/yoons_pennmedicine_upenn_edu/EUWD-eGwtr5FrsLEynw97UYBrlikFXEqDmClwt6g_AooWQ>

I also had a same error with 10kb resolution data. Here, I send you the bedpe file of chr19. Thanks,

Sora

From: YaqiangCao notifications@github.com Sent: Thursday, November 12, 2020 7:49 PM To: YaqiangCao/cLoops cLoops@noreply.github.com Cc: Yoon, Sora Sora.Yoon@Pennmedicine.upenn.edu; Author < author@noreply.github.com> Subject: [External] Re: [YaqiangCao/cLoops] ERROR: no inter-ligation PETs detected for eps 5000 minPts 50, can't model the distance cutoff, continue anyway (#24)

Yes, the .bedpe file.

On Thu, Nov 12, 2020 at 7:44 PM Sora Yoon (윤소라) < notifications@github.com>

wrote:

You mean the .bedpe file?? Sure, I will do that.

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