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comparison tophat_wrapper.xml @ 1:6eaefb5f755a

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Update Tophat URLs in help text.
author Nate Coraor <nate@bx.psu.edu>
date Mon, 17 Nov 2014 11:23:25 -0500
parents 1030acbecce6
children 8afd8a379d5f
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0:1030acbecce6 1:6eaefb5f755a
483 <help> 483 <help>
484 **Tophat Overview** 484 **Tophat Overview**
485 485
486 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, and then analyzes the mapping results to identify splice junctions between exons. Please cite: Trapnell, C., Pachter, L. and Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009). 486 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, and then analyzes the mapping results to identify splice junctions between exons. Please cite: Trapnell, C., Pachter, L. and Salzberg, S.L. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25, 1105-1111 (2009).
487 487
488 .. _Tophat: http://tophat.cbcb.umd.edu/ 488 .. _Tophat: http://ccb.jhu.edu/software/tophat/
489 489
490 ------ 490 ------
491 491
492 **Know what you are doing** 492 **Know what you are doing**
493 493
494 .. class:: warningmark 494 .. class:: warningmark
495 495
496 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. 496 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.
497 497
498 .. __: http://tophat.cbcb.umd.edu/manual.html 498 .. __: http://ccb.jhu.edu/software/tophat/manual.shtml
499 499
500 ------ 500 ------
501 501
502 **Input formats** 502 **Input formats**
503 503