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ngs_sequence_alignment_and_variant_calling [2014/11/26 14:57] sebastien.renaut |
ngs_sequence_alignment_and_variant_calling [2014/11/26 14:58] (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. | ||
