Tag Archives: coding

Saturday 11/23/13

Posted on November 23, 2013 by admin

10:00a – 11:00p STORM2 Helping Guipeng and Ruobo get set up on STORM2. Cell staining prepping cells for hybridizaton. last row (4 coverslips) forgot to add last rinse of PBS. Cells dried out. Coverslips tossed. cells into formamide, ready for … Continue reading →

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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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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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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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Wednesday 11/13/2013

Posted on November 13, 2013 by admin

10:00a – 7:15p Other Reply to BJ with final corrections / proofs Deep sequencing analysis scatterplot correlations on log10 scale Coding Interesting matlab fact: Nested functions have access to the parent workspace. Got CIGAR and MD parser from Jeff to … Continue reading →

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Protected: project 2 update

Posted on November 10, 2013 by admin

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Saturday 11/09/13

Posted on November 9, 2013 by admin

8:30a – 7:30p, 8:30p – 11:30p (remotely) Goals Write to Alvaro (done) Reply to Zenklusen (done) Continue analysis of MiSeq Results (in process) write to Jeff to get gene list (done) repeat RT reaction with more enzyme (done) Work on … Continue reading →

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