Category Archives: software

How to install linux software without root privileges

HPC cluster users rarely have root privileges for installing new software. Default location for installation is usually /usr/bin/, but our user directories are usually located somewhere else like /home/ljcohen/ or /mnt/home/ljcohen/. So, what are you supposed to do when you … Continue reading

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Error with HTSeq

Running HTSeq to get raw read counts associated with chromosomal positions/annotated genes from sorted .bam files: Error occurred when processing SAM input (record #30675291 in file {PATH}/tophat/Exp-1-Basal/accepted_hits.sorted.bam): Maximum alignment buffer size exceeded while pairing SAM alignments. [Exception type: ValueError, raised … Continue reading

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Genomics Analysis Tools

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

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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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Python is cool.

Some Python links: http://pycogent.org/ http://nbviewer.ipython.org/ http://nbviewer.ipython.org/github/CamDavidsonPilon/Probabilistic-Programming-and-Bayesian-Methods-for-Hackers/blob/master/Chapter1_Introduction/Chapter1_Introduction.ipynb https://github.com/ipython/ipython/wiki/A-gallery-of-interesting-IPython-Notebooks

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