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ngs_sequence_alignment_and_variant_calling [2014/11/26 09:57]
sebastien.renaut
ngs_sequence_alignment_and_variant_calling [2014/11/26 09:58] (current)
sebastien.renaut [Bioinformatics tools geared specifically towards gene expression (RNAseq) analyses]
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 ==== Bioinformatics tools geared specifically towards gene expression (RNAseq) analyses ==== ==== Bioinformatics tools geared specifically towards gene expression (RNAseq) analyses ====
    * [[http://​ccb.jhu.edu/​software/​tophat/​index.shtml|tophat]] -Aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. Usefull for analysing splice variants and their expression from NGS datasets    * [[http://​ccb.jhu.edu/​software/​tophat/​index.shtml|tophat]] -Aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie, and then analyzes the mapping results to identify splice junctions between exons. Usefull for analysing splice variants and their expression from NGS datasets
-   * There are also several R packages listed [[http://​qcbs.ca/​wiki/​resources_for_r#R Packages for Genetics and Sequence Analyses|here]] are specifically geared towards gene expression analyses+   * There are also several R packages listed [[http://​qcbs.ca/​wiki/​resources_for_r|here]] are specifically geared towards gene expression analyses
 ==== All-in-one proprietary software ==== ==== All-in-one proprietary software ====
   * [[http://​www.geneious.com/​|geneious]] ​ -Comprehensive bioinformatics software platform.   * [[http://​www.geneious.com/​|geneious]] ​ -Comprehensive bioinformatics software platform.