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comparison tophat2_wrapper.xml @ 1:ae06af1118dc

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Update Tophat URLs in help text.
author Nate Coraor <nate@bx.psu.edu>
date Mon, 17 Nov 2014 11:23:41 -0500
parents ffa30bedbee3
children da1f39fe14bc
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0:ffa30bedbee3 1:ae06af1118dc
453 **Tophat Overview** 453 **Tophat Overview**
454 454
455 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 455 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
456 of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36, 2013. 456 of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol 14:R36, 2013.
457 457
458 .. _Tophat: http://tophat.cbcb.umd.edu/ 458 .. _Tophat: http://ccb.jhu.edu/software/tophat/
459 459
460 ------ 460 ------
461 461
462 **Know what you are doing** 462 **Know what you are doing**
463 463
464 .. class:: warningmark 464 .. class:: warningmark
465 465
466 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. 466 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.
467 467
468 .. __: http://tophat.cbcb.umd.edu/manual.html 468 .. __: http://ccb.jhu.edu/software/tophat/manual.shtml
469 469
470 ------ 470 ------
471 471
472 **Input formats** 472 **Input formats**
473 473