RSEQtools - Revision history

Asboner: /* sam2mrf */

2013-04-22T14:08:49Z

sam2mrf

← Older revision		Revision as of 14:08, 22 April 2013
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	<center>[[#top\|Top]]</center>		<center>[[#top\|Top]]</center>

			==== mrfSorter ====

			mrfSorter sort each MRF line according to its coordinate format, i.e. the left-most coordinate would be reported first, regardless of strand.

			'''Usage''':

			mrfSorter

			* Inputs: Takes [[#MRF\|MRF]] format from STDIN
			* Outputs: Reports [[#MRF\|MRF]] to STDOUT
			* ''Required arguments''
			** None
			* ''Optional arguments''
			** None

			Example: <pre> mrfSorter <file.mrf > file.sorted.mrf </pre>

			<br>

	==== sam2mrf ====		==== sam2mrf ====

Asboner: /* sam2mrf */

2013-04-22T13:55:47Z

sam2mrf

← Older revision		Revision as of 13:55, 22 April 2013
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	** None		** None

	Please note that for paired-end data, sam2mrf requires the mate pairs to be on subsequent lines. You may want to sort the [[#SAM\|SAM]] file first.		Please note that for paired-end data, sam2mrf requires the mate pairs to be on subsequent lines. You may want to sort the [[#SAM\|SAM]] file first. Please note that you would need to run mrfSorter after sam2mrf to make a valid MRF file.

	Example: <pre>sort -r file.sam \| ~~sam2mrf~~ > file.mrf </pre>		Example: <pre>samtools sort file.sam file.sorted; sam2mrf < file.sorted.sam \| mrfSorter > file.mrf </pre>

	<br>		<br>

Asboner: /* singleExport2mrf */

2011-11-03T12:55:30Z

singleExport2mrf

← Older revision		Revision as of 12:55, 3 November 2011
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	<br>		<br>
	'''Note''': If a splice junction library is used during the alignment step, it is important that the splice junction library was generated by createSpliceJunctionLibrary and that its file name included 'splice' or 'junction'. Otherwise, singleExport2mrf will not be able to convert the splice junction coordinates correctly.		'''Note''': If a splice junction library is used during the alignment step, it is important that the splice junction library was generated by createSpliceJunctionLibrary and that its file name included 'splice' or 'junction'. Otherwise, singleExport2mrf will not be able to convert the splice junction coordinates correctly.
			<br>
			The output includes sequences and quality scores. If one wants the alignment only:
			singleExport2mrf < file.export.txt \| cut -f1 > file.mrf
	<br>		<br>

Asboner: /* singleExport2mrf */

2011-11-03T11:06:06Z

singleExport2mrf

← Older revision		Revision as of 11:06, 3 November 2011
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	** None		** None
	<br>		<br>
	'''Note''': If a splice junction library is used during the alignment step, it is important that the splice junction library was generated by createSpliceJunctionLibrary. Otherwise, singleExport2mrf will not be able to convert the splice junction coordinates correctly.		'''Note''': If a splice junction library is used during the alignment step, it is important that the splice junction library was generated by createSpliceJunctionLibrary and that its file name included 'splice' or 'junction'. Otherwise, singleExport2mrf will not be able to convert the splice junction coordinates correctly.

	<br>		<br>

Asboner: /* mrf2wig */

2011-04-18T17:43:27Z

mrf2wig

← Older revision		Revision as of 17:43, 18 April 2011
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	'''Usage''':		'''Usage''':

	mrf2wig <prefix> [~~doNotNormailze~~]		mrf2wig <prefix> [doNotNormalize]

	* Inputs: Takes [[#MRF\|MRF]] from STDIN.		* Inputs: Takes [[#MRF\|MRF]] from STDIN.
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	<center>[[#top\|Top]]</center>		<center>[[#top\|Top]]</center>

	==== mrf2gff ====		==== mrf2gff ====

Lukas.habegger at 15:20, 1 February 2011

2011-02-01T15:20:34Z

← Older revision		Revision as of 15:20, 1 February 2011
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	'''Usage''':		'''Usage''':

	mrf2wig <prefix> [~~counts~~]		mrf2wig <prefix> [doNotNormailze]

	* Inputs: Takes [[#MRF\|MRF]] from STDIN.		* Inputs: Takes [[#MRF\|MRF]] from STDIN.
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	** prefix - specifies the prefix used to generate the output files. The following naming convention is used: prefix_chrXXX.wig		** prefix - specifies the prefix used to generate the output files. The following naming convention is used: prefix_chrXXX.wig
	* ''Optional arguments''		* ''Optional arguments''
	** ~~counts~~ - ~~do not normalize values, report raw~~ counts ~~int the [[#WIG\|WIG]] file instead~~		** doNotNormailze - the counts are NOT normalized

	<br>		<br>

Lukas.habegger at 06:32, 8 December 2010

2010-12-08T06:32:19Z

← Older revision		Revision as of 06:32, 8 December 2010
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	<br>		<br>


	== Citation ==		== Citation ==

Lukas.habegger: /* Citation */

2010-12-08T06:31:10Z

Citation

← Older revision		Revision as of 06:31, 8 December 2010
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	== Citation ==		== Citation ==

	Lukas Habegger, Andrea Sboner, Tara A. Gianoulis, Joel Rozowsky, Ashish Agarwal, Michael Snyder, Mark Gerstein. RSEQtools: A modular framework to analyze RNA-Seq data using compact, anonymized data summaries. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq643?ijkey=GSZOpzLAEOqJtJ4&keytype=ref ~~'''~~Bioinformatics~~'''~~] 2010,		Lukas Habegger, Andrea Sboner, Tara A. Gianoulis, Joel Rozowsky, Ashish Agarwal, Michael Snyder, Mark Gerstein. '''RSEQtools: A modular framework to analyze RNA-Seq data using compact, anonymized data summaries'''. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq643?ijkey=GSZOpzLAEOqJtJ4&keytype=ref <i>Bioinformatics</i>] 2010,
	doi: 10.1093/bioinformatics/btq643		doi: 10.1093/bioinformatics/btq643

	<br>		<br>


	== Overview ==		== Overview ==

Lukas.habegger at 06:29, 8 December 2010

2010-12-08T06:29:48Z

← Older revision		Revision as of 06:29, 8 December 2010
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	== ~~Citation~~ ==		== Introduction ==

			The advent of next-generation sequencing for functional genomics has given rise to quantities of sequence information that are often so large that they are difficult to handle. Moreover, sequence reads from a specific individual can contain sufficient information to potentially identify that person, raising significant privacy concerns. In order to address these issues we have developed the Mapped Read Format (MRF), a compact data summary format for both short and long read alignments that enables the anonymization of confi-dential sequence information, while allowing one to still carry out many functional genomics studies. We have developed a suite of tools that uses this format for the analysis of RNA-Seq experiments. RSEQtools consists of a set of modules that perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads, and segmenting that signal into actively transcribed regions. In addition to the anonymization afforded by this format it also facilitates the decoupling of the alignment of reads from downstream analyses.

	Lukas Habegger, Andrea Sboner, Tara A. Gianoulis, Joel Rozowsky, Ashish Agarwal, Michael Snyder, Mark Gerstein. RSEQtools: A modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics 2010,		<br>
	~~doi: 10.1093/bioinformatics/btq643~~

	*contributed equally

	== ~~Introduction~~ ==		== Citation ==

	~~The advent of next-generation sequencing for functional genomics has given rise to quantities of sequence information that are often so large that they are difficult to handle~~. ~~Moreover~~, ~~sequence reads from a specific individual can contain sufficient information to potentially identify that person~~, ~~raising significant privacy concerns. In order to address these issues we have developed the Mapped Read Format (MRF)~~, ~~a compact data summary format for both short and long read alignments that enables the anonymization of confi-dential sequence information~~, ~~while allowing one~~ to ~~still carry out many functional genomics studies. We have developed a suite of tools that uses this format for the analysis of~~ RNA-Seq ~~experiments~~. ~~RSEQtools consists of a set of modules that perform common tasks such as calculating gene expression values, generating signal tracks of mapped reads~~, and segmenting that signal into actively transcribed regions. In addition to the anonymization afforded by this format it also facilitates the decoupling of the alignment of reads from downstream analyses.		Lukas Habegger, Andrea Sboner, Tara A. Gianoulis, Joel Rozowsky, Ashish Agarwal, Michael Snyder, Mark Gerstein. RSEQtools: A modular framework to analyze RNA-Seq data using compact, anonymized data summaries. [http://bioinformatics.oxfordjournals.org/cgi/content/abstract/btq643?ijkey=GSZOpzLAEOqJtJ4&keytype=ref '''Bioinformatics'''] 2010,
			doi: 10.1093/bioinformatics/btq643

	<br>		<br>


	== Overview ==		== Overview ==

Lukas.habegger: /* Citation */

2010-12-08T06:25:14Z

Citation

← Older revision		Revision as of 06:25, 8 December 2010
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	== Citation ==		== Citation ==

	Lukas Habegger, Andrea Sboner, Tara A. Gianoulis, Joel Rozowsky, Ashish Agarwal, Michael Snyder, Mark Gerstein. RSEQtools: A modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics 2010,		Lukas Habegger, Andrea Sboner, Tara A. Gianoulis, Joel Rozowsky, Ashish Agarwal, Michael Snyder, Mark Gerstein. RSEQtools: A modular framework to analyze RNA-Seq data using compact, anonymized data summaries. Bioinformatics 2010,
	doi: 10.1093/bioinformatics/btq643		doi: 10.1093/bioinformatics/btq643

	*contributed equally		*contributed equally


	== Introduction ==		== Introduction ==