comparison tophat2_wrapper.xml @ 1:ae06af1118dc

Update Tophat URLs in help text.

0:ffa30bedbee3

**Tophat Overview**

TopHat_ is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie(2), and then analyzes the mapping results to identify splice junctions between exons. Please cite: Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, and Salzberg SL. TopHat2: accurate alignment
of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36, 2013.

.. _Tophat: http://tophat.cbcb.umd.edu/
        
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**Know what you are doing**

.. class:: warningmark

There is no such thing (yet) as an automated gearshift in splice junction identification. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.

.. __: http://tophat.cbcb.umd.edu/manual.html

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**Input formats**

1:ae06af1118dc

**Tophat Overview**

TopHat_ is a fast splice junction mapper for RNA-Seq reads. It aligns RNA-Seq reads to mammalian-sized genomes using the ultra high-throughput short read aligner Bowtie(2), and then analyzes the mapping results to identify splice junctions between exons. Please cite: Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, and Salzberg SL. TopHat2: accurate alignment
of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36, 2013.

.. _Tophat: http://ccb.jhu.edu/software/tophat/
        
------

**Know what you are doing**

.. class:: warningmark

There is no such thing (yet) as an automated gearshift in splice junction identification. It is all like stick-shift driving in San Francisco. In other words, running this tool with default parameters will probably not give you meaningful results. A way to deal with this is to **understand** the parameters by carefully reading the `documentation`__ and experimenting. Fortunately, Galaxy makes experimenting easy.

.. __: http://ccb.jhu.edu/software/tophat/manual.shtml

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**Input formats**