QPLOT - Revision history

Ppwhite: /* Source Code Distribution */

2017-02-02T15:42:20Z

Source Code Distribution

← Older revision		Revision as of 11:42, 2 February 2017
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	== Source Code Distribution ==		== Source Code Distribution ==

	We provide a source code only download in [http://~~www~~.sph.umich.edu/~~csg~~/zhanxw/software/qplot/qplot-source.20130627.tar.gz qplot-source.20130627.tar.gz]. Optionally, you can download example file and/or data file:		We provide a source code only download in [http://csg.sph.umich.edu//zhanxw/software/qplot/qplot-source.20130627.tar.gz qplot-source.20130627.tar.gz]. Optionally, you can download example file and/or data file:

	[http://~~www~~.sph.umich.edu/~~csg~~/zhanxw/software/qplot/qplot-example.tar.gz example]: example input file, and expected outputs if you following the [[#Built-in example \| direction]].		[http://csg.sph.umich.edu//zhanxw/software/qplot/qplot-example.tar.gz example]: example input file, and expected outputs if you following the [[#Built-in example \| direction]].

	[http://~~www~~.sph.umich.edu/~~csg~~/zhanxw/software/qplot/qplot-data.tar.gz resources data]: necessary input files for qplot, including NCBI human genome build v37, dbSNP 130, and pre-computed GC file with windows size 100.		[http://csg.sph.umich.edu//zhanxw/software/qplot/qplot-data.tar.gz resources data]: necessary input files for qplot, including NCBI human genome build v37, dbSNP 130, and pre-computed GC file with windows size 100.

	You can put above file(s) in the same folder and follow these steps:		You can put above file(s) in the same folder and follow these steps:

Ppwhite: /* Binary Download */

2017-02-02T15:41:33Z

Binary Download

← Older revision		Revision as of 11:41, 2 February 2017
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	== Binary Download ==		== Binary Download ==

	We have prepared a pre-compiled (under Ubuntu) qplot along with source code . You can download it from: [http://~~www~~.sph.umich.edu/~~csg~~/zhanxw/software/qplot/qplot.20130627.tar.gz qplot.20130627.tar.gz (File Size: 1.7G)]		We have prepared a pre-compiled (under Ubuntu) qplot along with source code . You can download it from: [http://csg.sph.umich.edu//zhanxw/software/qplot/qplot.20130627.tar.gz qplot.20130627.tar.gz (File Size: 1.7G)]

	The executable file is under qplot/bin/qplot.		The executable file is under qplot/bin/qplot.

Mktrost: /* Parameters */

2015-02-23T14:13:15Z

Parameters

← Older revision		Revision as of 10:13, 23 February 2015
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	* Input file options :		* Input file options :

	BAM files are ~~compress by~~ BGZF ~~algorithm~~ and it should contain EOF by default. QPLOT will by default stop working ~~when~~ it does not ~~found~~ a valid EOF ~~tag~~ inside BAM files.		BAM files are compressed using BGZF and should contain the EOF indicator by default. QPLOT will, by default, stop working if it does not find a valid EOF indicator inside the BAM files.
	However, you can force QPLOT to continue ~~process~~ using --noeof. But you should be aware the input files may be corrupted.		However, you can force QPLOT to continue processing BAM files without an EOF indicator using --noeof. But you should be aware the input files may be corrupted.

Mktrost: /* Parameters */

2015-02-23T14:11:14Z

Parameters

← Older revision		Revision as of 10:11, 23 February 2015
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	or		or
	--qcfail_keep		--qcfail_keep


	*Records to process		*Records to process
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	'''NOTE''' In order for this to work, the lane info has to be encoded in the read name such that the lane number is the second field with the delimiter ":".		'''NOTE''' In order for this to work, the lane info has to be encoded in the read name such that the lane number is the second field with the delimiter ":".


	* Read group to process :		* Read group to process :

	~~Read~~ group option can restrict qplot to process a subset of reads. For example, if BAM ~~contain~~ the following @RG tags:		The read group option can restrict qplot to process a subset of reads. For example, if the BAM contains the following @RG tags:

	@RG ID:UM0348_1:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM		@RG ID:UM0348_1:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM
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	@RG ID:UM0360_4:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM		@RG ID:UM0360_4:1 PL:ILLUMINA LB:M5390 SM:M5390 CN:UM

	~~If specify nothing or not using "--readGroup",~~ QPLOT by default ~~will~~ process all reads;		QPLOT will by default (without specifying --readgroup) process all reads.
	If specify "--readGroup UM0348", then only read ~~group~~ UM0348_1, UM_0348_2, UM_0348_3, UM_0348_4 will be processed;
	If specify "--readGroup UM0348_1", then only one read group UM0348_1 will be processed.		If you specify "--readGroup UM0348", then only read groups UM0348_1, UM_0348_2, UM_0348_3, UM_0348_4 will be processed.

			If you specify "--readGroup UM0348_1", then only one read group, UM0348_1, will be processed.


	* Input file options :		* Input file options :
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	Qplot will exclude reads with lower mapping qualities than the user specified parameter, <code>--minMapQuality</code>. By default, mapped reads with all mapping quality will be included in the analysis.		Qplot will exclude reads with lower mapping qualities than the user specified parameter, <code>--minMapQuality</code>. By default, mapped reads with all mapping quality will be included in the analysis.


	*Region list		*Region list

Hmkang: /* Citing QPLOT */

2013-11-26T19:48:52Z

Citing QPLOT

← Older revision		Revision as of 15:48, 26 November 2013
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	= Citing QPLOT =		= Citing QPLOT =

	If you found QPLOT useful and wants to cite in your paper, please ~~refer to~~ the information below.		If you found QPLOT useful and wants to cite in your paper, please copy and paste the information below.

	* Bingshan Li, Xiaowei Zhan, Mary-Kate Wing, Paul Anderson, Hyun Min Kang, and Goncalo R. Abecasis, “QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data,” BioMed Research International, vol. 2013, Article ID 865181, 4 pages, 2013. doi:10.1155/2013/865181 http://www.hindawi.com/journals/bmri/2013/865181/		* Bingshan Li, Xiaowei Zhan, Mary-Kate Wing, Paul Anderson, Hyun Min Kang, and Goncalo R. Abecasis, “QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data,” BioMed Research International, vol. 2013, Article ID 865181, 4 pages, 2013. doi:10.1155/2013/865181 http://www.hindawi.com/journals/bmri/2013/865181/

Hmkang: /* Citing QPLOT */

2013-11-26T19:48:36Z

Citing QPLOT

← Older revision		Revision as of 15:48, 26 November 2013
Line 9:		Line 9:
	If you found QPLOT useful and wants to cite in your paper, please refer to the information below.		If you found QPLOT useful and wants to cite in your paper, please refer to the information below.

	Bingshan Li, Xiaowei Zhan, Mary-Kate Wing, Paul Anderson, Hyun Min Kang, and Goncalo R. Abecasis, “QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data,” BioMed Research International, vol. 2013, Article ID 865181, 4 pages, 2013. doi:10.1155/2013/865181 http://www.hindawi.com/journals/bmri/2013/865181/		* Bingshan Li, Xiaowei Zhan, Mary-Kate Wing, Paul Anderson, Hyun Min Kang, and Goncalo R. Abecasis, “QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data,” BioMed Research International, vol. 2013, Article ID 865181, 4 pages, 2013. doi:10.1155/2013/865181 http://www.hindawi.com/journals/bmri/2013/865181/

	= Where to Find It =		= Where to Find It =

Hmkang: /* Citing QPLOT */

2013-11-26T19:48:25Z

Citing QPLOT

← Older revision		Revision as of 15:48, 26 November 2013
Line 9:		Line 9:
	If you found QPLOT useful and wants to cite in your paper, please refer to the information below.		If you found QPLOT useful and wants to cite in your paper, please refer to the information below.

	Bingshan Li, Xiaowei Zhan, Mary-Kate Wing, Paul Anderson, Hyun Min Kang, and Goncalo R. Abecasis, “QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data,” BioMed Research International, vol. 2013, Article ID 865181, 4 pages, 2013. doi:10.1155/2013/865181 http://www.hindawi.com/journals/bmri/2013/865181/		Bingshan Li, Xiaowei Zhan, Mary-Kate Wing, Paul Anderson, Hyun Min Kang, and Goncalo R. Abecasis, “QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data,” BioMed Research International, vol. 2013, Article ID 865181, 4 pages, 2013. doi:10.1155/2013/865181 http://www.hindawi.com/journals/bmri/2013/865181/

	= Where to Find It =		= Where to Find It =

Hmkang: /* Introduction */

2013-11-26T19:48:15Z

Introduction

← Older revision		Revision as of 15:48, 26 November 2013
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	In the following sections, we will guide you through: [[#Where to Find It \|how to obtain qplot]], [[#Usage \|how to use qplot]], [[#Built-in example \|example outputs]], [[#anchorOfInteractiveQplot \|interactive diagnostic plots]], and [[#Diagnose sequencing quality \|real applications]] in which qplot has helped identify sequencing problems.		In the following sections, we will guide you through: [[#Where to Find It \|how to obtain qplot]], [[#Usage \|how to use qplot]], [[#Built-in example \|example outputs]], [[#anchorOfInteractiveQplot \|interactive diagnostic plots]], and [[#Diagnose sequencing quality \|real applications]] in which qplot has helped identify sequencing problems.

			= Citing QPLOT =

			If you found QPLOT useful and wants to cite in your paper, please refer to the information below.

			Bingshan Li, Xiaowei Zhan, Mary-Kate Wing, Paul Anderson, Hyun Min Kang, and Goncalo R. Abecasis, “QPLOT: A Quality Assessment Tool for Next Generation Sequencing Data,” BioMed Research International, vol. 2013, Article ID 865181, 4 pages, 2013. doi:10.1155/2013/865181 http://www.hindawi.com/journals/bmri/2013/865181/

	= Where to Find It =		= Where to Find It =

Ben Lerch: /* Parameters */

2013-08-06T16:53:23Z

Parameters

← Older revision		Revision as of 12:53, 6 August 2013
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	BAM files are compress by BGZF algorithm and it should contain EOF by default. QPLOT will by default stop working when it does not found a valid EOF tag inside BAM files.		BAM files are compress by BGZF algorithm and it should contain EOF by default. QPLOT will by default stop working when it does not found a valid EOF tag inside BAM files.
	However, you can force QPLOT to continue process using --noeof. But you should be ~~award~~ the input files may be corrupted.		However, you can force QPLOT to continue process using --noeof. But you should be aware the input files may be corrupted.

Zhanxw at 18:09, 29 June 2013

2013-06-29T18:09:31Z

← Older revision		Revision as of 14:09, 29 June 2013
Line 15:		Line 15:
	== Binary Download ==		== Binary Download ==

	We have prepared a pre-compiled (under Ubuntu) qplot along with source code . You can download it from: [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot.~~20130619~~.tar.gz qplot.~~20130619~~.tar.gz (File Size: 1.7G)]		We have prepared a pre-compiled (under Ubuntu) qplot along with source code . You can download it from: [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot.20130627.tar.gz qplot.20130627.tar.gz (File Size: 1.7G)]

	The executable file is under qplot/bin/qplot.		The executable file is under qplot/bin/qplot.
Line 25:		Line 25:
	== Source Code Distribution ==		== Source Code Distribution ==

	We provide a source code only download in [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-source.~~20130619~~.tar.gz qplot-source.~~20130619~~.tar.gz]. Optionally, you can download example file and/or data file:		We provide a source code only download in [http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-source.20130627.tar.gz qplot-source.20130627.tar.gz]. Optionally, you can download example file and/or data file:

	[http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-example.tar.gz example]: example input file, and expected outputs if you following the [[#Built-in example \| direction]].		[http://www.sph.umich.edu/csg/zhanxw/software/qplot/qplot-example.tar.gz example]: example input file, and expected outputs if you following the [[#Built-in example \| direction]].
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	* 1. Unarchive downloaded file		* 1. Unarchive downloaded file
	tar zvxf qplot-source.~~20130619~~.tar.gz		tar zvxf qplot-source.20130627.tar.gz

	A new folder ''qplot'' will be created.		A new folder ''qplot'' will be created.