Monthly Archives: November 2013

Friday 11/22/13

Posted on November 22, 2013 by admin

9:45a – 11:50a (remotely) 12:00p – 7:10p Genomics A549 whole cell data finished running cufflinks. Bottom half of genes are empty / all have zero FKPM (chr12 on). attempting to run cufflinks 2.1 centos6 version on cytosol BAM file directly … Continue reading →

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Thursday 11/21/13

Posted on November 21, 2013 by admin

9:30a – 11:15p Meetings working on slides for chat with Mike. meeting with Mike Levine Levine seminar at HMS Genomics installed cufflinks on local scratch folder successfully (? or not) ran on Rep1 data from ENCODE. All FPKM and coverage … Continue reading →

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Levine Seminar

Posted on November 21, 2013 by admin

recently become interested in questions of transcriptional precision 100bp core promoter snail = 100_/10 polII read count (‘pausing score’) sog = 40 5 ths = 15+/- 4 weakly paused ths very small patches of twist expressing cells invaginate. moderately paused … Continue reading →

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Wednesday 11/20/13

Posted on November 20, 2013 by admin

10:15a – 10:00p Goals prepare slides for chat with Levine Reply to SW Genome Analysis Mi Seq analysis of off target hybridization sequence bias New strategy: Generate new fasta file with the entry ID number as the first 5 digits … Continue reading →

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Tuesday 11/19/13

Posted on November 19, 2013 by admin

9:15a – 1:00a Goals Slides for meeting with Levine Chromatin STORM analysis Analyze D11 region cells should arrive today — start in culture Library 3 design Library 3 observation: short green regions (<50 kb, basically everything not near a centromere/telomere) … Continue reading →

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Monday 11/18/13

Posted on November 18, 2013 by admin

9:00a – 8:30p, 10:00p – 11:45p (remotely) Assorted Tasks Submitted final BIRS workshop report to BIRS directors Install updates on lab servers Cajal and Tuck and reboot servers. Ph project launch simulations with matched parameters. PhM conc variation Chromatin colors … Continue reading →

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Sunday 11/17/13

Posted on November 17, 2013 by admin

10:00a – 7:30p, 10:15p – 12:00a Ph Project Coding Cleaning up Ph simulation codes moving more stuff to functions sped up pivotMove removed loop in plotting function Most computation time now taken up by Mex Function call in pdist. see … Continue reading →

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Saturday 11/16/13

Posted on November 16, 2013 by admin

6:30p -8:00p Polymer simulation PRC1 simulations finished without error Need to optimize axes and binning for distribution plots. Free Polymer radius of gyration calibration still running, (last update, round 6 1024 link polymer). polynomial fits (don’t extrapolate well without taking … Continue reading →

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Friday 11/15/13

Posted on November 15, 2013 by admin

7:30a – 11:15a General stuff installed windows updates on Monet installed new RAM (now 32GB) sent (final?) version of Banff report to co-organizers. Send to BIRS on Mon. Chromatin simulations functionalizing chromatin simulation code attempting to increase simulation speed distance … Continue reading →

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Protected: project2

Posted on November 15, 2013 by admin

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