Monthly Archives: January 2014

Genomics Workshop (Week 2, Day 4) – QIIME and Metgenomics Analyses

Daniel McDonald from Dr. Rob Knight’s lab, U. Colorado Some links: http://www.earthmicrobiome.org/ http://www.hmpdacc.org/ QIIME analysis tool, using iPython notebook: http://evomics.org/learning/genomics/metagenomics/metagenomics-laboratories/ Data files: http://qiime.org/home_static/dataFiles.html from this study: http://www.ncbi.nlm.nih.gov/pubmed/21624126 additional info: http://www.ncbi.nlm.nih.gov/pubmed/20534432 argument for using iPython notebook: http://www.ncbi.nlm.nih.gov/pubmed/23096404 iPython notebook: http://ipython.org/ipython-doc/stable/interactive/notebook.html

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Genomics Analysis Tools

http://www.broadinstitute.org/software/igv/home

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Workshop on Genomics (Week 2, Day 3) – Transcriptomics

Dr. Manual Garber: Lecture slides: http://evomicsorg.wpengine.netdna-cdn.com/wp-content/uploads/2013/03/evomics_krumlov_2014.pdf Exercises: http://evomics.org/learning/genomics/transcriptomics/#part1 Exercise 1: Prepare for genomic alignment (when there is reference genome) Exercise 2: Genome alignment of RNA-seq reads Question: What percent of reads were mapped for each library? ubuntu@ip-10-151-69-171:~/transcriptomics/tophat$ cat th.quant.ctrl1/align_summary.txt th.quant.ctrl2/align_summary.txt … Continue reading

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PYTHONPATH

To run graphing graphics in Python: flcellogrl@flcellogrl:~$ pip install matplotlib Installing Python modules with virtualenv or pip: http://www.bdnyc.org/2012/09/17/editing-pythonpath-to-import-modules/ Logical and neat directory structure will make your own, your computer’s and your collaborators’ lives much easier. My recommendation: Create a master … Continue reading

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Workshop on Genomics (Week 2, Day 2) – Metagenomics

Interesting argument for the importance of social media. Rapid analysis of data for diagnosis of public health-related issues before publications/reports can be written/submitted. Also, public record of conversations and advice that might help people learning. Dr. Nick Loman: http://pathogenomics.bham.ac.uk/blog/ http://www.flickr.com/photos/lpcohen/12066175364/Continue reading

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