15 May 2014

How I start a bioinformatics project

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Phil Ashton tweeted a link to a paper about how to set up a bioinformatics project file hierarchy: " A Quick Guide to Organizing Compu...
12 May 2014

Generating wikipedia semantic links from a pubmed-id

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In " Building a biomedical semantic network in Wikipedia with Semantic Wiki Links" (Database . 2012 Mar 20;2012) Benjamin Good ...
30 January 2014

Parallelizing #RStats using #make

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In the current post, I'll show how to use R as the main SHELL of GNU-Make instead of using a classical linux shell like 'bash...
1 comment:

Mapping the UCSC/Web-Sequences to a world map.

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People at the UCSC have recently released a new track for the GenomeBrowser We BLATted the Internet! The DNA sequences from 40 billion webp...
12 December 2013

Inside Jvarkit: view BAM, cut, stats, head, tail, shuffle, downsample, group-by-gene VCFs...

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Here are a few tools I recently wrote (and reinvented) for Jvarkit . BamViewGui a simple java-Swing-based BAM viewer. VcfShuffle Shuff...
2 comments:
20 November 2013

Inside Jvarkit: Shrink your fastqs by 40% by aligning them to REF before compression.

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BamToFastq is an implementation of https://twitter.com/DNAntonie/status/402909852277932032 " Shrink your FASTQ.bz2 files by 40+% using...
2 comments:
30 October 2013

GNU Make: saving the versions of the tools using 'order-only-prerequisites' : my notebook

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Rule 3 of "Ten Simple Rules for Reproducible Computational Research" . is : Archive the Exact Versions of All External Programs U...
1 comment:
25 October 2013

YES: "Choice of transcripts and software has a large effect on variant annotation"

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This post was inspired by Aaron Quinlan 's tweet: Poster 1485: variant annotation is harder than you think. transcript set matters (sur...
24 October 2013

PubMed Commons & Bioinformatics: a call for action

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NCBI pubmed Commons / @PubMedCommons is a new system that enables researchers to share their opinions about scientific publications. Resear...
1 comment:
23 October 2013

Inside the variation toolkit: Generating a structured document describing an Illumina directory.

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I wrote a tool named " Illuminadir " : it creates a structured ( JSON or XML ) representation of a directory containing som...