https://wiki.4dnucleome.org/ 2026-04-19T03:29:06-0700 https://wiki.4dnucleome.org/ https://wiki.4dnucleome.org/_media/wiki:favicon.ico text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:data_analysis:dawg-meeting-notes-20170518?rev=1745364087&do=diff DAWG Meeting Notes 20170518 (Burak: I did not keep detailed minutes; Here are a bunch of notes I scribbled. Feel free to edit. See Slides for figures.) Bottomline: * Different callers give very different results. * Callers vary by sizes of domain called and number vs. sequencing depth. text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:data_analysis:dawg-meeting-notes-20170601?rev=1745364087&do=diff DAWG Meeting Notes 20170601 Hi-C read filtering. Presentation by Anton, Max, Mirny Lab. (Minutes by Burak; Feel free to edit.) 4 types of filters * - PCR * - Dangling ends / self circles * - Poorly mapped reads (MAPQ) * - Random ligations (distance to restriction site) text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:data_analysis:dawg-meeting-notes-20170615?rev=1745364087&do=diff DAWG Meeting Notes 20170615 A. DCIC status and plans for reaching consensus - Picked 6 datasets to use for tool evaluation (IMR90 and GM12878) - Current pipeline implementation uses juicer for alignment and filtering, juicer and cooler for normalization text/html 2025-04-22T16:21:27-0700 Anonymous (anonymous@undisclosed.example.com) https://wiki.4dnucleome.org/4dn:phase1:data_analysis:dawg-meeting-notes-20170803?rev=1745364087&do=diff DAWG Meeting Notes 20170803 Comparison of Hi-C processing tools Burak Alver Reminder: We are planning to run: - fastq -> pairs (juicer) - pairs -> hic (juicer) - pairs -> cool (cooler) - export juicer normvectors and import to the cools. - export cooler normvectors and provide in juicebox format.