Tag Archives: genomics

Saturday 12/14/13

Posted on December 14, 2013 by admin

11:15a – 2:30p, 6:00p – 11:45p Coding matlab-storm test installation: created new ZhuangLab account Install for Guipeng. DaoSTORM objects to spaces in pathname. adding double quotes ” does not fix. library Prep New function (in Genomics Functions toolbox) function Seq … Continue reading →

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Thursday 12/05/13

Posted on December 5, 2013 by admin

9:30a – 12:20a Goals Restart analysis for project 2 Probe making: check PCRs, continue if good, restart if not. launch STORM analysis for last few days of imaging project 2 see notes. Chromatin Project Probe Making Test PCRs Clean, reorganize, … 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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Protected: project 2 to do

Posted on April 25, 2013 by admin

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Saturday 03/23/13

Posted on March 23, 2013 by admin

11:00 A Cell culture Moved cell to 28C incubator observe substantial cell debris in dish (dead cells from heat shock?) Genomics Installing OligoArray2.0 http://berry.engin.umich.edu/oligoarray2/ Need to install legacy BLAST. Installed. Need to install OligoArrayAux: http://mfold.rna.albany.edu/?q=DINAMelt/OligoArrayAux. Error with database in2 = … Continue reading →

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Friday 03/22/13

Posted on March 22, 2013 by admin

11:00 A – 7:30 P, 9:30P – 11:58 P Discussion recommend using homology-fused single labeled probes to test the double labeling efficiency for Hao’s experiment. reference call for Bryon Genomics cleaned up Genomics functions maxInterval.m maxIntervalBed.m added new function IntervalFuseGaps.m … Continue reading →

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Thursday 03/14/13

Posted on March 14, 2013 by admin

10:00 A – 7:40P, 8:30P-10:30P Genomics processing real vanSteensel data now Reading in data and converting to int8 data matrix for data compression.cellfun(@(x) int8(round(20*str2double(x))), data) seems to be running slower than looping the over the columns… Actually need single to … Continue reading →

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Wednesday 03/13/13

Posted on March 13, 2013 by admin

10:00 A – 9:30P, 11:00P – 12:55 A STORM Finish O/N run on STORM2 STORM Analysis Launch Analysis of all fab7 data collected on STORM2 — now running on Cajal in small batches. Finish configuring local repo on TUCK to … Continue reading →

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