TopHat - Revision history

Tanthony@uab.edu: /* Direct Use through SGE submit scripts */ changed /lustre/scratch/ to /scratch/user

2013-06-25T14:27:01Z

Direct Use through SGE submit scripts: changed /lustre/scratch/ to /scratch/user

← Older revision		Revision as of 14:27, 25 June 2013
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	<pre>		<pre>
	$ mkdir -p /~~lustre~~/~~scratch~~/USERNAME/jobs/tophat		$ mkdir -p /scratch/user/USERNAME/jobs/tophat
	$ cd /~~lustre~~/~~scratch~~/USERNAME/jobs/tophat		$ cd /scratch/user/USERNAME/jobs/tophat
	</pre>		</pre>

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	<pre>		<pre>
	$ module load module load galaxy/galaxy		$ module load module load galaxy/galaxy
	$ bowtie-build /~~lustre~~/~~scratch~~/USERNAME/jobs/tophat/example.fa example_bowtie_idx		$ bowtie-build /scratch/user/USERNAME/jobs/tophat/example.fa example_bowtie_idx
	</pre>		</pre>
	This builds the Bowtie index for the genome 'example'. You can also download the pre-built index file from other external sources.		This builds the Bowtie index for the genome 'example'. You can also download the pre-built index file from other external sources.

Pavgi@uab.edu: /* TopHat Tutorials */

2013-06-18T19:06:38Z

TopHat Tutorials

← Older revision		Revision as of 19:06, 18 June 2013
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	[[Category: NGS]][[Category:Bioinformatics]]		[[Category: NGS]][[Category:Software]][[Category:Bioinformatics]]

Pavgi@uab.edu: /* TopHat Tutorials */

2013-06-18T19:02:50Z

TopHat Tutorials

← Older revision		Revision as of 19:02, 18 June 2013
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	[[Category: NGS~~]][[Category:Software~~]][[Category:Bioinformatics]]		[[Category: NGS]][[Category:Bioinformatics]]

Tanthony@uab.edu: added category bioinformatics

2012-04-04T15:44:24Z

added category bioinformatics

← Older revision		Revision as of 15:44, 4 April 2012
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	[[Category: NGS]][[Category:Software]]		[[Category: NGS]][[Category:Software]][[Category:Bioinformatics]]

Tanthony@uab.edu: added category software

2012-04-04T14:19:19Z

added category software

← Older revision		Revision as of 14:19, 4 April 2012
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	[[Category: NGS]]		[[Category: NGS]][[Category:Software]]

Tanthony@uab.edu: /* TopHat Tutorials */

2011-08-03T16:20:53Z

TopHat Tutorials

← Older revision		Revision as of 16:20, 3 August 2011
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	== TopHat Tutorials ==		== TopHat Tutorials ==
	* TopHat Tutorials can be found at: http://tophat.cbcb.umd.edu/manual.html		* TopHat Tutorials can be found at: http://tophat.cbcb.umd.edu/manual.html
	* ~~Gromacs~~ Tutorials: http://icb.med.cornell.edu/wiki/index.php/Tophat_tutorial		* TopHat Tutorials: http://icb.med.cornell.edu/wiki/index.php/Tophat_tutorial


	[[Category: NGS]]		[[Category: NGS]]

Tanthony@uab.edu at 15:26, 3 August 2011

2011-08-03T15:26:45Z

← Older revision		Revision as of 15:26, 3 August 2011
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	[http://tophat.cbcb.umd.edu/ 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 [http://bowtie-bio.sourceforge.net/index.shtml Bowtie], and then analyzes the mapping results to identify splice junctions between exons.		[http://tophat.cbcb.umd.edu/ 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 [http://bowtie-bio.sourceforge.net/index.shtml Bowtie], and then analyzes the mapping results to identify splice junctions between exons.
	TopHat is a collaborative effort between the [http://cbcb.umd.edu/ University of Maryland Center for Bioinformatics and Computational Biology] and the University of California, Berkeley [http://math.berkeley.edu/ Departments of Mathematics] and [http://www.mcb.berkeley.edu/ Molecular and Cell Biology]
			TopHat is a collaborative effort between the [http://cbcb.umd.edu/ University of Maryland Center for Bioinformatics and Computational Biology] and the University of California, Berkeley [http://math.berkeley.edu/ Departments of Mathematics] and [http://www.mcb.berkeley.edu/ Molecular and Cell Biology].

	The latest stable release on [[Cheaha]] is 1.2.0 as part of the [http://main.g2.bx.psu.edu/ Galaxy] module. TopHat can run through the [http://galaxy.uabgrid.uab.edu/ UAB Galaxy] interface or directly on the cluster by submitting jobs to SGE.		The latest stable release on [[Cheaha]] is 1.2.0 as part of the [http://main.g2.bx.psu.edu/ Galaxy] module. TopHat can run through the [http://galaxy.uabgrid.uab.edu/ UAB Galaxy] interface or directly on the cluster by submitting jobs to SGE.

Tanthony@uab.edu at 15:24, 3 August 2011

2011-08-03T15:24:58Z

← Older revision		Revision as of 15:24, 3 August 2011
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	[http://tophat.cbcb.umd.edu/ 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 [http://bowtie-bio.sourceforge.net/index.shtml Bowtie], and then analyzes the mapping results to identify splice junctions between exons.		[http://tophat.cbcb.umd.edu/ 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 [http://bowtie-bio.sourceforge.net/index.shtml Bowtie], and then analyzes the mapping results to identify splice junctions between exons.
			TopHat is a collaborative effort between the [http://cbcb.umd.edu/ University of Maryland Center for Bioinformatics and Computational Biology] and the University of California, Berkeley [http://math.berkeley.edu/ Departments of Mathematics] and [http://www.mcb.berkeley.edu/ Molecular and Cell Biology]
	TopHat is a collaborative effort between the [http://cbcb.umd.edu/ University of Maryland Center for Bioinformatics and Computational Biology] and the University of California, Berkeley [http://math.berkeley.edu/ Departments of Mathematics] and [http://www.mcb.berkeley.edu/ Molecular and Cell Biology].


	The latest stable release on [[Cheaha]] is 1.2.0 as part of the [http://main.g2.bx.psu.edu/ Galaxy] module. TopHat can run through the [http://galaxy.uabgrid.uab.edu/ UAB Galaxy] interface or directly on the cluster by submitting jobs to SGE.		The latest stable release on [[Cheaha]] is 1.2.0 as part of the [http://main.g2.bx.psu.edu/ Galaxy] module. TopHat can run through the [http://galaxy.uabgrid.uab.edu/ UAB Galaxy] interface or directly on the cluster by submitting jobs to SGE.


	==Using TopHat==		==Using TopHat==
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	TopHat can be downloaded and installed on your desktop from http://tophat.cbcb.umd.edu/		TopHat can be downloaded and installed on your desktop from http://tophat.cbcb.umd.edu/

	~~Install~~ instructions for TopHat are available at: http://tophat.cbcb.umd.edu/tutorial.html		Installation instructions for TopHat are available at: http://tophat.cbcb.umd.edu/tutorial.html


	===TopHat on Cheaha===		===TopHat on Cheaha===
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	1. Direct use on the cluster using SGE submit scripts.		1. Direct use on the cluster using SGE submit scripts.
	2. TopHat use through the [http://galaxy.uabgrid.uab.edu/ UAB Galaxy] interface.		2. TopHat use through the [http://galaxy.uabgrid.uab.edu/ UAB Galaxy] interface.


	====Direct Use through SGE submit scripts ====		====Direct Use through SGE submit scripts ====
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	$ samtools view accepted_hits.bam		$ samtools view accepted_hits.bam
	</pre>		</pre>


	====Using the UAB Galaxy interface====		====Using the UAB Galaxy interface====
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	# Select reference genome and RNA sequence file		# Select reference genome and RNA sequence file
	# Execute		# Execute


	~~== TopHat Support ==~~
	~~In order to facilitate interaction among TopHat users, share experience, and provide peer-support UAB IT Research Computing will establish a TopHat-users group.~~

	== Galaxy support ==		== Galaxy support ==

Tanthony@uab.edu at 14:59, 3 August 2011

2011-08-03T14:59:45Z

← Older revision		Revision as of 14:59, 3 August 2011
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	* -N - job name		* -N - job name
	* -M - user email		* -M - user email
	* -pe smp numberOfProcessors (-pe smp 8 - run the code in parallel on 8 processors on the same node of Cheaha. Also, -pe smp 12 is the maximum available number of processors)		* -pe smp numberOfProcessors (-pe smp 8 - run the code in parallel on 8 processors on the same node of Cheaha.
			Also, -pe smp 12 is the maximum available number of processors)
	* -l vf to the maximum memory needed for each task		* -l vf to the maximum memory needed for each task
	* in the following example the genome is 'example', the reads are read1,read2, output will be written to testTophat/ folder. The -r parameter is the Mean Inner Distance between Mate Pairs for pair-ended library. This parameter can be left out for a single-ended library.		* In the following example the genome is 'example', the reads are read1,read2, output will be written to testTophat/ folder.
			The -r parameter is the Mean Inner Distance between Mate Pairs for pair-ended library.
			This parameter can be left out for a single-ended library.

	<pre>		<pre>

Tanthony@uab.edu: added -r single-ended and pair-ended in qsub scripts

2011-08-03T14:57:49Z

added -r single-ended and pair-ended in qsub scripts

← Older revision		Revision as of 14:57, 3 August 2011
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	* -pe smp numberOfProcessors (-pe smp 8 - run the code in parallel on 8 processors on the same node of Cheaha. Also, -pe smp 12 is the maximum available number of processors)		* -pe smp numberOfProcessors (-pe smp 8 - run the code in parallel on 8 processors on the same node of Cheaha. Also, -pe smp 12 is the maximum available number of processors)
	* -l vf to the maximum memory needed for each task		* -l vf to the maximum memory needed for each task
	* in the following example the genome is 'example', the reads are read1,read2, output will be written to testTophat/ folder		* in the following example the genome is 'example', the reads are read1,read2, output will be written to testTophat/ folder. The -r parameter is the Mean Inner Distance between Mate Pairs for pair-ended library. This parameter can be left out for a single-ended library.

	<pre>		<pre>