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: QIIME analysis tool, using iPython notebook: Data files: from this study: additional info: argument for using iPython notebook: iPython notebook:

Posted in Bioinformatics, Data Analyses, Python | Leave a comment

Genomics Analysis Tools

Posted in Bioinformatics, software | Leave a comment

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

Dr. Manual Garber: Lecture slides: Exercises: 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

Posted in Genomics Workshop | Leave a comment


To run graphing graphics in Python: flcellogrl@flcellogrl:~$ pip install matplotlib Installing Python modules with virtualenv or pip: 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

Posted in Genomics Workshop, Python | Leave a comment

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: reading

Posted in Bioinformatics, Genomics Workshop, software | Leave a comment