TopHat-IP is the TopHat tool at Galalaxy Pasteur. See links for TopHat. TopHat is a tool for splice-aware mapping of RNA-seq reads. The TopHat uses the Bowtie short read aligner tool (BWT-based algorithm) for the mapping whereafter it identifies intron-exon (splice) junctions. TopHat can use paired-end sequencing reads and parallel computation. (*BWT=Burrows–Wheeler transform)
RNA-Seq
Trapnell C, Pachter L, Salzberg SL "TopHat: discovering splice junctions with RNA-Seq." Bioinformatics. 2009 May 1;25(9):1105-11. Epub 2009 Mar 16. https://doi.org/10.1093/bioinformatics/btp120
PMID: 19289445
PMCID: PMC2672628
Afgan E, Baker D, van den Beek M, Blankenberg D, Bouvier D, Čech M, Chilton J, Clements D, Coraor N, Eberhard C, Grüning B, Guerler A, Hillman-Jackson J, Von Kuster G, Rasche E, Soranzo N, Turaga N, Taylor J, Nekrutenko A, Goecks J "The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update." Nucleic Acids Res. 2016 Jul 8;44(W1):W3-W10. https://doi.org/10.1093/nar/gkw343
PMID: 27137889
PMCID: PMC4987906
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