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Monthly Archives: February 2014
Thursday 02/27/14
10:00a – 11:15p Meetings (ski trip planning meeting) (10a-11a) team project planning meeting (11a-12p) Project 2 data analysis locate new data files run splitdax run STORM analysis on data and beads beads look low contrast but we’ll see. Literature: selected … Continue reading
Posted in Summaries
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Protected: project 2 planning meeting
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Posted in Genomics
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Wednesday 02/25/14
10:30a – 11:00p Chromatin Project Analysis Analysis of multi-color data quick look at G1-G2 data from 12-30. Almost complete overlap of regions. Current multi-color / adjacent region datasets: ‘Q:\2014-01-10_F11-7_F12-6’ ‘Q:\2014-01-10_G01-6_G02-7’ ‘Q:\2014-01-09_F05F06’ ‘Q:\2013-12-30_G1G2’ – 750 survived remarkably well. Should check buffer … Continue reading
Tuesday 02/25/14
11:00a – 11:30p Data compression (~11a-12p) troubleshooting beaddax averaging added some safety checks. System now checks to see if detected files for deletion contain the downsampled ds tag. If they do they won’t be deleted. System also checks if 561 … Continue reading
Posted in Summaries
Tagged cell culture, coding, database, Deep Sequencing
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Protected: Library Error Analysis by MiSeq
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Monday 02/24/14
(sick, working from home) Library3 prep continues running primer finding adding more filtering do a direct comparison on final 5 basepairs, reject all perfect matches, keep only unique ones. reran a few times to debug raising T min to 74C … Continue reading
organizing research documentation
My Current Scheme: Research Papers downloaded PDFs, a Mendeley ‘watched folder’ Paperwork list of suppliers, order forms for equipment, reimbursement forms, applications for grants / fellowships etc Protocols a github hosted repo of Markdown files Presentations conference talks / advisor … Continue reading
Posted in Research Planning
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dataset curation
Compressing Bead movies from the following data files ‘M:\2013-11-01_F07\splitdax’ ‘M:\2013-11-02_D11\splitdax’ ‘M:\2013-10-29_E10\splitdax’ ‘M:\2013-10-28_E08\splitdax’ ‘M:\2013-10-27_E01\splitdax’ ‘K:\2013-10-26_D12\splitdax’ ‘K:\2013-10-25_D11\splitdax’ ‘K:\2013-10-11_F10\splitdax’ ‘K:\2013-10-10_F11\splitdax’ ‘J:\2013-10-06_no405Primary\splitdax’ ‘J:\2013-10-05_E06\splitdax’ ‘J:\2013-10-04_G05\splitdax’ ‘J:\2013-10-03_E02\splitdax’ ‘J:\2013-10-02_D09\splitdax’ ‘J:\2013-10-01_G10\splitdax’ ‘H:\2013-10-09_F01V2\splitdax’ ‘H:\2013-10-07_F09\splitdax’ ‘H:\2013-09-24_F6-405\splitdax’ ‘H:\2013-09-23_F6\splitdax’ ‘H:\2013-09-09_G4\splitdax’ ‘H:\2013-09-05_G6\splitdax’ ‘H:\2013-09-04_G3\splitdax’ ‘H:\2013-09-02_G2\splitdax’ ‘H:\2013-08-22_Ubx\splitdax’ ‘H:\2013-08-21_AbdA\splitdax’ All 561quad_movies downsampled to 1 Hz, introduce … Continue reading
Protected: some analysis of Hao Lib3 and 4
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Friday 02/21/14
10:15a – 5:50p Chromatin Project Library 3 prep finish annotating new lib3 yellow green regions ran probe folding for yellow green regions Current probes (including 10 new black, 8 new blue): 91144 Deep Seq analysis Trying to understand why some … Continue reading