27 October 2016

Hello WDL ( Workflow Description Language )

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This is a quick note about my first WDL workflow (Workflow Description Language) https://software.broadinstitute.org/wdl/ . As a Makefil...
22 September 2016

Writing a Custom ReadFilter for the GATK, my notebook.

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The GATK contains a set of predefined read filters that "filter or transfer incoming SAM/BAM data files" : BadCigar BadMate Co...
09 September 2016

Playing with #magicblast, the #NCBI Short read mapper. My notebook

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NCBI MAGIC Blast was recently mentioned by BioMickWatson on twitter. Looks pretty cool. Perhaps once again the answer to all bfx questio...
1 comment:
27 May 2016

pubmed: extracting the 1st authors' gender and location who published in the Bioinformatics journal.

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In this post I'll get some statistics about the 1st authors in the "Bioinformatics" journal from pubmed. I'll extract thei...
21 May 2016

Playing with the @ORCID_Org / @ncbi_pubmed graph. My notebook.

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" ORCID provides a persistent digital identifier that distinguishes you from every other researcher and, through integration in key re...
17 May 2016

finding new intron-exon junctions using the public Encode RNASeq data

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I've been asked to look for some new / suspected / previously uncharacterized intron-exon junctions in public RNASeq data. I've use...
04 March 2016

Now in picard: two javascript-based tools filtering BAM and VCF files.

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SamJS and VCFFilterJS are two tools I wrote for jvarkit . Both tools use the embedded java javascript engine to filter BAM or VCF file. ...
1 comment:

Reading a VCF file faster with java 8, htsjdk and java.util.stream.Stream

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java 8 streams "support functional-style operations on streams of elements, such as map-reduce transformations on collections". I...
24 February 2016

Registering a tool in the @ELIXIREurope regisry using XML, XSLT, JSON and curl. My notebook.

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The Elixir Registry / pmid:26538599 "A portal to bioinformatics resources world-wide. With community support, the registry can become...
05 December 2015

Happy birthday my blog. You are now ten-year-old.

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Happy birthday my blog. You are now 10-year-old.
2 comments: