Bam read count - Revision history

Bingshan: /* Introduction */

2012-08-14T19:29:10Z

Introduction

← Older revision		Revision as of 15:29, 14 August 2012
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	== Introduction ==		== Introduction ==

	'''NOTE: ~~the~~ current version works only for single end reads. If the input bam file contains paired end sequences, reads from the same fragment will be counted independently'''		'''NOTE: The current version works only for single end reads. If the input bam file contains paired end sequences, reads from the same fragment will be counted independently'''

	* The tools calculates the read count for each region in the input list of regions from a BAM file, and also outputs the normalized read count as Read Per Million Mapped Reads per Kilobases (RPKM). To correct for the bias of the read count due to GC bias, it will also output the GC content of each region along with the total reads mapped to the corresponding GC content bins. By providing this statistic, the extent of GC bias can be investigated and if excessive bias is observed this statistic can be used to correct the global GC bias.		* The tools calculates the read count for each region in the input list of regions from a BAM file, and also outputs the normalized read count as Read Per Million Mapped Reads per Kilobases (RPKM). To correct for the bias of the read count due to GC bias, it will also output the GC content of each region along with the total reads mapped to the corresponding GC content bins. By providing this statistic, the extent of GC bias can be investigated and if excessive bias is observed this statistic can be used to correct the global GC bias.

Bingshan: /* Introduction */

2012-08-14T19:28:50Z

Introduction

← Older revision		Revision as of 15:28, 14 August 2012
Line 1:		Line 1:
	== Introduction ==		== Introduction ==

	'''NOTE: the current version works only for single end reads'''		'''NOTE: the current version works only for single end reads. If the input bam file contains paired end sequences, reads from the same fragment will be counted independently'''

	* The tools calculates the read count for each region in the input list of regions from a BAM file, and also outputs the normalized read count as Read Per Million Mapped Reads per Kilobases (RPKM). To correct for the bias of the read count due to GC bias, it will also output the GC ~~contact~~ of each region along with the total reads mapped to the corresponding GC content bins. By providing this statistic, the extent of GC bias can be investigated and if excessive bias is observed this statistic can be used to correct the global GC bias.		* The tools calculates the read count for each region in the input list of regions from a BAM file, and also outputs the normalized read count as Read Per Million Mapped Reads per Kilobases (RPKM). To correct for the bias of the read count due to GC bias, it will also output the GC content of each region along with the total reads mapped to the corresponding GC content bins. By providing this statistic, the extent of GC bias can be investigated and if excessive bias is observed this statistic can be used to correct the global GC bias.

	* This tool was initially developed for RNA-seq data to quantify gene/exon expression but can also be used for other purposes as well.		* This tool was initially developed for RNA-seq data to quantify gene/exon expression but can also be used for other purposes as well.

Bingshan: /* Introduction */

2012-08-14T19:27:00Z

Introduction

← Older revision		Revision as of 15:27, 14 August 2012
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	== Introduction ==		== Introduction ==

	''NOTE: it works only for single end reads''		'''NOTE: the current version works only for single end reads'''

	* The tools calculates the read count for each region in the input list of regions from a BAM file, and also outputs the normalized read count as Read Per Million Mapped Reads per Kilobases (RPKM). To correct for the bias of the read count due to GC bias, it will also output the GC contact of each region along with the total reads mapped to the corresponding GC content bins. By providing this statistic, the extent of GC bias can be investigated and if excessive bias is observed this statistic can be used to correct the global GC bias.		* The tools calculates the read count for each region in the input list of regions from a BAM file, and also outputs the normalized read count as Read Per Million Mapped Reads per Kilobases (RPKM). To correct for the bias of the read count due to GC bias, it will also output the GC contact of each region along with the total reads mapped to the corresponding GC content bins. By providing this statistic, the extent of GC bias can be investigated and if excessive bias is observed this statistic can be used to correct the global GC bias.

Bingshan: /* Introduction */

2012-08-14T19:26:30Z

Introduction

← Older revision		Revision as of 15:26, 14 August 2012
Line 1:		Line 1:
	== Introduction ==		== Introduction ==

	NOTE: it works only for single end reads		''NOTE: it works only for single end reads''

	* The tools calculates the read count for each region in the input list of regions from a BAM file, and also outputs the normalized read count as Read Per Million Mapped Reads per Kilobases (RPKM). To correct for the bias of the read count due to GC bias, it will also output the GC contact of each region along with the total reads mapped to the corresponding GC content bins. By providing this statistic, the extent of GC bias can be investigated and if excessive bias is observed this statistic can be used to correct the global GC bias.		* The tools calculates the read count for each region in the input list of regions from a BAM file, and also outputs the normalized read count as Read Per Million Mapped Reads per Kilobases (RPKM). To correct for the bias of the read count due to GC bias, it will also output the GC contact of each region along with the total reads mapped to the corresponding GC content bins. By providing this statistic, the extent of GC bias can be investigated and if excessive bias is observed this statistic can be used to correct the global GC bias.

Bingshan: /* Introduction */

2012-08-14T19:25:43Z

Introduction

← Older revision		Revision as of 15:25, 14 August 2012
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	== Introduction ==		== Introduction ==

			NOTE: it works only for single end reads

	* The tools calculates the read count for each region in the input list of regions from a BAM file, and also outputs the normalized read count as Read Per Million Mapped Reads per Kilobases (RPKM). To correct for the bias of the read count due to GC bias, it will also output the GC contact of each region along with the total reads mapped to the corresponding GC content bins. By providing this statistic, the extent of GC bias can be investigated and if excessive bias is observed this statistic can be used to correct the global GC bias.		* The tools calculates the read count for each region in the input list of regions from a BAM file, and also outputs the normalized read count as Read Per Million Mapped Reads per Kilobases (RPKM). To correct for the bias of the read count due to GC bias, it will also output the GC contact of each region along with the total reads mapped to the corresponding GC content bins. By providing this statistic, the extent of GC bias can be investigated and if excessive bias is observed this statistic can be used to correct the global GC bias.

Bingshan: /* Download */

2012-08-03T19:48:47Z

Download

← Older revision		Revision as of 15:48, 3 August 2012
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	== Download ==		== Download ==
	The latest version of source code v0.01 can be [[Media:readcount.0.01.tar.gz \| downloaded]] here.		The latest version of source code v0.01 can be [[Media:readcount.0.01.tar.gz \| downloaded]] here. To compile, cd readcount.0.01/ and type make. The executable is under bin/ directory.

	== Contact ==		== Contact ==

Bingshan: /* Download */

2012-08-03T19:44:04Z

Download

← Older revision		Revision as of 15:44, 3 August 2012
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	== Download ==		== Download ==
	The latest version of source code v0.01 can be [[Media:readcount.0.01.tar.gz \| downloaded]] here.		The latest version of source code v0.01 can be [[Media:readcount.0.01.tar.gz \| downloaded]] here.


	== Contact ==		== Contact ==

Bingshan at 19:43, 3 August 2012

2012-08-03T19:43:15Z

← Older revision		Revision as of 15:43, 3 August 2012
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	AACSL:5 2171 15 0.780 0.359 49.65 443653		AACSL:5 2171 15 0.780 0.359 49.65 443653
	AADAC:3 1607 172 8.949 5.569 38.39 468603		AADAC:3 1607 172 8.949 5.569 38.39 468603

			== Download ==
			The latest version of source code v0.01 can be [[Media:readcount.0.01.tar.gz \| downloaded]] here.


	== Contact ==		== Contact ==

Bingshan: /* Introduction */

2012-08-03T19:38:20Z

Introduction

← Older revision		Revision as of 15:38, 3 August 2012
Line 1:		Line 1:
	== Introduction ==		== Introduction ==

	* The tools calculates the read count for each region in the input list of regions from a BAM file, and also outputs the normalized read count as Read Per Million Mapped Reads per Kilobases (RPKM). To correct for the bias of the read count due to GC bias, it will also output the GC contact of each region along with the total reads mapped to the corresponding GC content bins. Bu providing this ~~statistics~~, the extent of GC bias can be investigated and if excessive bias is observed this statistic can be used to correct the global GC bias.		* The tools calculates the read count for each region in the input list of regions from a BAM file, and also outputs the normalized read count as Read Per Million Mapped Reads per Kilobases (RPKM). To correct for the bias of the read count due to GC bias, it will also output the GC contact of each region along with the total reads mapped to the corresponding GC content bins. By providing this statistic, the extent of GC bias can be investigated and if excessive bias is observed this statistic can be used to correct the global GC bias.

	* This tool was initially developed for RNA-seq data to quantify gene/exon expression but can also be used for other ~~sequences~~ as well.		* This tool was initially developed for RNA-seq data to quantify gene/exon expression but can also be used for other purposes as well.

	== Usage ==		== Usage ==

Bingshan: /* Other options */

2012-08-03T19:36:54Z

Other options

← Older revision		Revision as of 15:36, 3 August 2012
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	--min_overlap : minimum number of bases overlapping an input region to consider that the read is in the region.		--min_overlap : minimum number of bases overlapping an input region to consider that the read is in the region.
			--min_map_quality : reads with map quality below this number will be ignored
	--uniq : If a read is mapped to multiple regions (e.g. exons) this read will be counted only once toward the read count in the gene		--uniq : If a read is mapped to multiple regions (e.g. exons) this read will be counted only once toward the read count in the gene
	--norm_by_mapped2target : The RPM and RPKM will be normalized by reads mapped only to target regions. Default is to use all mapped reads in a bam file.		--norm_by_mapped2target : The RPM and RPKM will be normalized by reads mapped only to target regions. Default is to use all mapped reads in a bam file.