Talk:QPLOT - Revision history

Zhanxw at 20:20, 21 November 2011

2011-11-21T20:20:32Z

← Older revision		Revision as of 16:20, 21 November 2011
Line 2:		Line 2:

	(1) Empirical vs reported Phred score:		(1) Empirical vs reported Phred score:

	Conditioning on the reported base quality, we count the total time of bases that matches or not matches the reference genome, and thus calculate the empirical quality by : -10 * log10 ( 1 - total # of mismatched / total bases) . In following cases, we will not use that bases for calculating empirical qualities:		Conditioning on the reported base quality, we count the total time of bases that matches or not matches the reference genome, and thus calculate the empirical quality by : -10 * log10 ( 1 - total # of mismatched / total bases) . In following cases, we will not use that bases for calculating empirical qualities:

Line 13:		Line 14:

	(2) Empirical Phred score by cycle:		(2) Empirical Phred score by cycle:

	Conditioning on read cycle (e.g. first base, second base... be cautious using quality trimmed reads or bar-coded reads, as the real cycle may differ), we calculate empirical quality as above.		Conditioning on read cycle (e.g. first base, second base... be cautious using quality trimmed reads or bar-coded reads, as the real cycle may differ), we calculate empirical quality as above.
	If specifying --region, only bases falling in the target regions will be calculated.		If specifying --region, only bases falling in the target regions will be calculated.

	(3) Mean depth vs. GC		(3) Mean depth vs. GC

	We will count depth for whole genome or specified region (--region).		We will count depth for whole genome or specified region (--region).
	Default GC window size is 100.		Default GC window size is 100.
Line 24:		Line 27:

	(4) Insert size		(4) Insert size

	For mapped paired-end reads, the insert size distribution will be ploted. Otherwise, this graph would be empty.		For mapped paired-end reads, the insert size distribution will be ploted. Otherwise, this graph would be empty.
	Specifying --region will not affect this graph.		Specifying --region will not affect this graph.

	(5) Empirical Q20 bases count by cycle		(5) Empirical Q20 bases count by cycle

	We count the number of Q20 bases (base qualities that are larger than 20) conditioning on cycle number.		We count the number of Q20 bases (base qualities that are larger than 20) conditioning on cycle number.
	If specifying --regions, only bases in the target regions will be calculated. In such case, some reads will have their head and trail outside of the region. Thus you will likely to see a parabolic shape.		If specifying --regions, only bases in the target regions will be calculated. In such case, some reads will have their head and trail outside of the region. Thus you will likely to see a parabolic shape.

	(6) Flag stats		(6) Flag stats

	We count the number of reads in these categories: total, mapped, paired, proper paired, duplicated, QC failed.		We count the number of reads in these categories: total, mapped, paired, proper paired, duplicated, QC failed.
	These categories are determined by FLAG field from each BAM file.		These categories are determined by FLAG field from each BAM file.

	(7) Mean depth of sequencing		(7) Mean depth of sequencing
	Total mapped bases divided by total number of positions that are covered by at least one base.
			Total mapped bases divided by total number of positions that are covered by at least one base. The y-axis, percentage is calculated by sites divided by total sites (e.g. for whole genome, it's the total length; for target sequencing, it's the total length of all targeted region).

	(8) Empirical Q20 count		(8) Empirical Q20 count

	We examine each base by its reported base quality, if that reported base quality corresponds to empirical base quality bettern Phred score 20, than we will count once as Q20 base.		We examine each base by its reported base quality, if that reported base quality corresponds to empirical base quality bettern Phred score 20, than we will count once as Q20 base.

Zhanxw at 17:53, 29 August 2011

2011-08-29T17:53:41Z

← Older revision		Revision as of 13:53, 29 August 2011
Line 1:		Line 1:
	Qplot process each aligned bam files.		Qplot process each aligned bam files.

	(1) Empirical vs reported Phred score:		(1) Empirical vs reported Phred score:
	Conditioning on the reported base quality, we count the total time of bases that matches or not matches the reference genome, and thus calculate the empirical quality by : -10 * log10 ( 1 - total # of mismatched / total bases) . In following cases, we will not use that bases for calculating empirical qualities:		Conditioning on the reported base quality, we count the total time of bases that matches or not matches the reference genome, and thus calculate the empirical quality by : -10 * log10 ( 1 - total # of mismatched / total bases) . In following cases, we will not use that bases for calculating empirical qualities:

	(a) 'N' for either sequence read or reference genome,		(a) 'N' for either sequence read or reference genome,

	(b) sequence reads that have sam flags including duplicated, unmapped		(b) sequence reads that have sam flags including duplicated, unmapped

	(c) overlapping dbSNP sites (if dbSNP position file provided)		(c) overlapping dbSNP sites (if dbSNP position file provided)

	If specifying --regions, only bases in the target regions will be calculated.		If specifying --regions, only bases in the target regions will be calculated.

Zhanxw: Created page with 'Qplot process each aligned bam files. (1) Empirical vs reported Phred score: Conditioning on the reported base quality, we count the total time of bases that matches or not match…'

2011-08-29T17:53:11Z

Created page with 'Qplot process each aligned bam files. (1) Empirical vs reported Phred score: Conditioning on the reported base quality, we count the total time of bases that matches or not match…'

New page

Qplot process each aligned bam files.
(1) Empirical vs reported Phred score:
Conditioning on the reported base quality, we count the total time of bases that matches or not matches the reference genome, and thus calculate the empirical quality by : -10 * log10 ( 1 - total # of mismatched / total bases) . In following cases, we will not use that bases for calculating empirical qualities:
(a) 'N' for either sequence read or reference genome,
(b) sequence reads that have sam flags including duplicated, unmapped
(c) overlapping dbSNP sites (if dbSNP position file provided)
If specifying --regions, only bases in the target regions will be calculated.

(2) Empirical Phred score by cycle:
Conditioning on read cycle (e.g. first base, second base... be cautious using quality trimmed reads or bar-coded reads, as the real cycle may differ), we calculate empirical quality as above.
If specifying --region, only bases falling in the target regions will be calculated.

(3) Mean depth vs. GC
We will count depth for whole genome or specified region (--region).
Default GC window size is 100.
For each position, we know its GC counts should between 0-100.
Across the whole genome of specified region, conditioning on the above GC counts, we calculated the total depth.
Then divides by frequency of positions where they have the same GC counts in the windows and divide by the coverage (total mapped bases divided by total covered positions, aka. see (7) Mean depth of sequencing)

(4) Insert size
For mapped paired-end reads, the insert size distribution will be ploted. Otherwise, this graph would be empty.
Specifying --region will not affect this graph.

(5) Empirical Q20 bases count by cycle
We count the number of Q20 bases (base qualities that are larger than 20) conditioning on cycle number.
If specifying --regions, only bases in the target regions will be calculated. In such case, some reads will have their head and trail outside of the region. Thus you will likely to see a parabolic shape.

(6) Flag stats
We count the number of reads in these categories: total, mapped, paired, proper paired, duplicated, QC failed.
These categories are determined by FLAG field from each BAM file.

(7) Mean depth of sequencing
Total mapped bases divided by total number of positions that are covered by at least one base.

(8) Empirical Q20 count
We examine each base by its reported base quality, if that reported base quality corresponds to empirical base quality bettern Phred score 20, than we will count once as Q20 base.