pyGenomeTracks Operation on Hi-C Maps

[matteozoia4]

Dear pyGenomeTracks providers,

is there the option to overlay Hi-C maps and normalise - enlightening differential activity(interaction) between Hi-C Maps?

Many thanks!

[lldelisle]

Dear @matteozoia4 , I am not sure I understand your question. Do you want to display something like a differential heatmap or ratio heatmap like in panel B, C, D of this figure? Or do you want to highlight an interaction identified like in panel A of this figure? Or something else.

[matteozoia4]

Dear Lucille,

yes indeed, I would like to perform subtraction between Hi-C maps of different tissues (panel B, C, D).

Best,

Matteo

Zoia Matteo, Ph.D. Student Gene Regulation & Cardiac Development

Marco Osterwalder Laboratory Department for BioMedical Research (DBMR) University of Bern Lab 369, Murtenstrasse 28 CH - 3008 Bern SWITZERLAND

---

Da: Lucille Delisle @.***> Inviato: mercoledì, 5. gennaio 2022 13:57:34 A: deeptools/pyGenomeTracks Cc: Zoia, Matteo (DBMR); Mention Oggetto: Re: [deeptools/pyGenomeTracks] pyGenomeTracks Operation on Hi-C Maps (Issue #368)

Dear @matteozoia4https://github.com/matteozoia4 , I am not sure I understand your question. Do you want to display something like a differential heatmap or ratio heatmap like in panel B, C, D of this figurehttp://genesdev.cshlp.org/content/35/21-22/1490/F3.expansion.html? Or do you want to highlight an interaction identified like in panel A of this figurehttp://genesdev.cshlp.org/content/suppl/2021/10/26/gad.348934.121.DC1/Supplemental_Fig_S8.pdf? Or something else.

— Reply to this email directly, view it on GitHubhttps://github.com/deeptools/pyGenomeTracks/issues/368#issuecomment-1005663487, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUBHT3CBXPNUKQNNPIBUNTTUUQ535ANCNFSM5LJR37WQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.***>

[lldelisle]

Then, I recommend to use hicCompareMatrices from the HiCExplorer tool suite (also developped by deeptools) on your matrices and then display the result with pyGenomeTracks.

[matteozoia4]

Many thanks I will look into this!

Best regards and thank you,

Matteo

Zoia Matteo, Ph.D. Student Gene Regulation & Cardiac Development

Marco Osterwalder Laboratory Department for BioMedical Research (DBMR) University of Bern Lab 369, Murtenstrasse 28 CH - 3008 Bern SWITZERLAND

---

Da: Lucille Delisle @.***> Inviato: mercoledì, 5. gennaio 2022 14:19:07 A: deeptools/pyGenomeTracks Cc: Zoia, Matteo (DBMR); Mention Oggetto: Re: [deeptools/pyGenomeTracks] pyGenomeTracks Operation on Hi-C Maps (Issue #368)

Then, I recommend to use hicCompareMatriceshttps://hicexplorer.readthedocs.io/en/latest/content/tools/hicCompareMatrices.html from the HiCExplorer tool suite (also developped by deeptools) on your matrices and then display the result with pyGenomeTracks.

— Reply to this email directly, view it on GitHubhttps://github.com/deeptools/pyGenomeTracks/issues/368#issuecomment-1005678566, or unsubscribehttps://github.com/notifications/unsubscribe-auth/AUBHT3F7YWVCFQQTENP57DTUURAMXANCNFSM5LJR37WQ. Triage notifications on the go with GitHub Mobile for iOShttps://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 or Androidhttps://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub. You are receiving this because you were mentioned.Message ID: @.***>

[lldelisle]

You are welcome.