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deeptools / HiCExplorer

HiCExplorer is a powerful and easy to use set of tools to process, normalize and visualize Hi-C data.
https://hicexplorer.readthedocs.org
GNU General Public License v3.0
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hicAggregateContacts --mode inter-chr issue #758

Open Drosophilid opened 3 years ago

Drosophilid commented 3 years ago

Hi @joachimwolff, I always impressed by this powerful tool :)

Recently I was trying to use hicAggregateContacts parameter to see the long-range interaction (for specific regions) between chromosomes using parameter --mode inter-chr. It took several hours to finish the job and end up without any output. I was wondering if I don't understand this paprmeter correctly or is there anything wrong with my command. Below is the command I have used.

Python 2.7.5

/apps/hicexplorer/3.7.1/bin/hicAggregateContacts

command#1 /apps/hicexplorer/3.7.1/bin/hicAggregateContacts --matrix em.10kb_matrix.h5 --BED region.bed -out em.inter.pdf --outFileContactPairs em.inter.tab --numberOfBins 30 --mode inter-chr --transform obs/exp --plotType 3d --operationType mean --chromosomes 2 3 4 X command#2 /apps/hicexplorer/3.7.1/bin/hicAggregateContacts --matrix em.10kb_matrix.h5 --BED region.2.bed --BED2 region.4.bed -out em.inter.pdf --outFileContactPairs em.inter.tab --numberOfBins 30 --mode inter-chr --transform obs/exp --plotType 3d --operationType mean

Any suggestions or recommendations will be highly appreciated.

error produced: Screen Shot 2021-10-15 at 4 38 42 PM

joachimwolff commented 3 years ago

Please use a recent Python version like 3.6, 3.7 or 3.8. We dropped the support for Python 2.7 two or three years ago. Maybe that is the reason for your issue.

Drosophilid @.***> schrieb am Fr. 15. Okt. 2021 um 16:40:

Hi @joachimwolff https://github.com/joachimwolff, I always impressed by this powerful tool :)

Recently I was trying to use hicAggregateContacts parameter to see the long-range interaction (for specific regions) between chromosomes using parameter --mode inter-chr. It took several hours to finish the job and end up without any output. I was wondering if I don't understand this paprmeter correctly or is there anything wrong with my command. Below is the command I have used.

Python 2.7.5

/apps/hicexplorer/3.7.1/bin/hicAggregateContacts

command#1 /apps/hicexplorer/3.7.1/bin/hicAggregateContacts --matrix em.10kb_matrix.h5 --BED region.bed -out em.inter.pdf --outFileContactPairs em.inter.tab --numberOfBins 30 --mode inter-chr --transform obs/exp --plotType 3d --operationType mean --chromosomes 2 3 4 X command#2 /apps/hicexplorer/3.7.1/bin/hicAggregateContacts --matrix em.10kb_matrix.h5 --BED region.2.bed --BED2 region.4.bed -out em.inter.pdf --outFileContactPairs em.inter.tab --numberOfBins 30 --mode inter-chr --transform obs/exp --plotType 3d --operationType mean

Any suggestions or recommendations will be highly appreciated.

error produced: [image: Screen Shot 2021-10-15 at 4 38 42 PM] https://user-images.githubusercontent.com/64106867/137505491-c9292069-bf43-45dc-8a0b-28bb90d7f85f.png

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/deeptools/HiCExplorer/issues/758, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADGQCABFAACGS45TESQBJ53UHA4L3ANCNFSM5GCD3XXA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub.

-- Joachim Wolff M.Sc. Computer Science Chair for Bioinformatics Department of Computer Science Albert-Ludwigs-University Freiburg Georges-Koehler-Allee 079 D-79110 Freiburg

http://www.bioinf.uni-freiburg.de

Drosophilid commented 3 years ago

Please use a recent Python version like 3.6, 3.7 or 3.8. We dropped the support for Python 2.7 two or three years ago. Maybe that is the reason for your issue. Drosophilid @.***> schrieb am Fr. 15. Okt. 2021 um 16:40: Hi @joachimwolff https://github.com/joachimwolff, I always impressed by this powerful tool :) Recently I was trying to use hicAggregateContacts parameter to see the long-range interaction (for specific regions) between chromosomes using parameter --mode inter-chr. It took several hours to finish the job and end up without any output. I was wondering if I don't understand this paprmeter correctly or is there anything wrong with my command. Below is the command I have used. #Python 2.7.5 #/apps/hicexplorer/3.7.1/bin/hicAggregateContacts command#1 /apps/hicexplorer/3.7.1/bin/hicAggregateContacts --matrix em.10kb_matrix.h5 --BED region.bed -out em.inter.pdf --outFileContactPairs em.inter.tab --numberOfBins 30 --mode inter-chr --transform obs/exp --plotType 3d --operationType mean --chromosomes 2 3 4 X command#2 /apps/hicexplorer/3.7.1/bin/hicAggregateContacts --matrix em.10kb_matrix.h5 --BED region.2.bed --BED2 region.4.bed -out em.inter.pdf --outFileContactPairs em.inter.tab --numberOfBins 30 --mode inter-chr --transform obs/exp --plotType 3d --operationType mean Any suggestions or recommendations will be highly appreciated. error produced: [image: Screen Shot 2021-10-15 at 4 38 42 PM] https://user-images.githubusercontent.com/64106867/137505491-c9292069-bf43-45dc-8a0b-28bb90d7f85f.png — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#758>, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADGQCABFAACGS45TESQBJ53UHA4L3ANCNFSM5GCD3XXA . Triage notifications on the go with GitHub Mobile for iOS https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Android https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. -- Joachim Wolff M.Sc. Computer Science Chair for Bioinformatics Department of Computer Science Albert-Ludwigs-University Freiburg Georges-Koehler-Allee 079 D-79110 Freiburg http://www.bioinf.uni-freiburg.de

Hi @joachimwolff, I also tried with Python version 3.9.0 and got the same error. Screen Shot 2021-10-17 at 10 45 15 AM

mujahida87 commented 3 years ago

Hi, @joachimwolff I also have a similar issue like @Drosophilid. I am interested to check hicAggregateContacts for cis-elements between the chromosomes (inter-chr mode), using default parameters. It took 3 days to finish the job but at the I don't get any output. I'm using hicExplorer version 3.7.1 and python 3.9.0. Do you have any suggestion to use the inter-chr mode feature? It will be of great help. Thanks

joachimwolff commented 3 years ago

@LeilyR Can you have a look at this issue?

mujahida87 commented 3 years ago

Hi @LeilyR can you please suggest something for above #758 Thank you

mujahida87 commented 2 years ago

Hi@LeilyR, a polite reminder. can you please check the issue #758

LeilyR commented 2 years ago

The reason is that you most likely have a very low amount of contacts between chromosomes on your matrix, so the obs/exp function underlying the --transform obs/exp returns all zero. Also, it could well be that you have zero contacts in those 3 chromosomes which you were selected. But first, I 'd suggest you trying it without transformation