Evaluating a Read Mapper on Simulated Data - Revision history

Goncalo at 03:19, 9 September 2010

2010-09-09T03:19:51Z

Zhanxw: /* Available Test Datasets */

2010-02-17T00:12:36Z

Available Test Datasets

← Older revision		Revision as of 20:12, 16 February 2010
Line 52:		Line 52:
	*Format		*Format

	; Both base space and color space		Both base space and color space
	; Both single end and paired end, and paired end reads are given insert size 1500.
	; Forward strand and reverse strand are randomly assign with probability 1/2		Both single end and paired end, and paired end reads are given insert size 1500.

			Forward strand and reverse strand are randomly assign with probability 1/2

	* Tag		* Tag

	@2:12345:F:SE:Exact		@2:12345:F:SE:Exact

	@2:12345:F:SE:SNP:2,12345,A,G;2,12346,T,C		@2:12345:F:SE:SNP:2,12345,A,G;2,12346,T,C

	@2:12345:F:PE+offset:SNP:2,12345,A,G (ref is A, read is G)		@2:12345:F:PE+offset:SNP:2,12345,A,G (ref is A, read is G)

	@2:12345:F:PE+offset:Indel:25M30D5M		@2:12345:F:PE+offset:Indel:25M30D5M

	* File Naming		* File Naming

	BS_SE_EXACT_1M_50		BS_SE_EXACT_1M_50

	BS_SE_SNP1_1M_50		BS_SE_SNP1_1M_50

	CS_SE_INDEL1_1M		CS_SE_INDEL1_1M

	CS_SE_INDEL30_1M		CS_SE_INDEL30_1M

	CS_SE_INDEL200_1M		CS_SE_INDEL200_1M

	CS_SE_DEL1_1M		CS_SE_DEL1_1M

	For PE, appending "_1" and "_2", e.g.:		For PE, appending "_1" and "_2", e.g.:

	PE_EXACT_1M_1		PE_EXACT_1M_1

	PE_EXACT_1M_2		PE_EXACT_1M_2

Line 90:		Line 104:

	* Example		* Example

	For illumina (from Sanger, 108mer hap1 test file):		For illumina (from Sanger, 108mer hap1 test file):

	Example:		Example:
	<pre>		<pre>
Line 117:		Line 133:

	Conclusion:		Conclusion:

	If the first read is forward, then itself is the same as reference sequence and the second read is reverse complement to the reference sequence.		If the first read is forward, then itself is the same as reference sequence and the second read is reverse complement to the reference sequence.

	If the first read is backward, then itself is reverse complement to the reference genome and the second read is the same as the reference sequence.		If the first read is backward, then itself is reverse complement to the reference genome and the second read is the same as the reference sequence.

	The first strand always position can always obtain from tag, first two fields (seperated by colon).		The first strand always position can always obtain from tag, first two fields (seperated by colon).

	The second strand position is first strand position plus the offset.		The second strand position is first strand position plus the offset.

Zhanxw: /* Bulk statistics result */

2010-02-16T15:52:45Z

Bulk statistics result

← Older revision		Revision as of 11:52, 16 February 2010
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	<pre>		<pre>
	BWA(second) Karma(second) Scenarios		BWA(second) Karma(second) Scenarios
	~~2594 7182 BS_SE_DEL200_1000000_50~~.fastq		7561 4638 BS_PE_DEL200_1000000_50_?.fastq
	~~2641 -1 BS_SE_DEL30_1000000_50~~.fastq		7548 4677 BS_PE_DEL30_1000000_50_?.fastq
	~~2355 -1 BS_SE_DEL5_1000000_50~~.fastq		7225 4730 BS_PE_DEL5_1000000_50_?.fastq
	~~441 7941 BS_SE_EXACT_1000000_50~~.fastq		975 6531 BS_PE_EXACT_1000000_50_?.fastq
	~~809 282 BS_SE_INDEL30_1000000_50~~.fastq		1726 793 BS_PE_INDEL30_1000000_50_?.fastq
	~~2217 -1 BS_SE_INDEL5_1000000_50~~.fastq		6199 4140 BS_PE_INDEL5_1000000_50_?.fastq
	~~645 7206 BS_SE_SNP1_1000000_50~~.fastq		1193 4949 BS_PE_SNP1_1000000_50_?.fastq
	~~1102 -1 BS_SE_SNP2_1000000_50~~.fastq		1646 4513 BS_PE_SNP2_1000000_50_?.fastq
	~~1142 -1 BS_SE_SNP3_1000000_50~~.fastq		2064 4089 BS_PE_SNP3_1000000_50_?.fastq
	~~6536 8874 BS_PE_DEL200_1000000_50_?~~.fastq		2594 3707 BS_SE_DEL200_1000000_50.fastq
	~~6699 9017 BS_PE_DEL30_1000000_50_?~~.fastq		2641 3942 BS_SE_DEL30_1000000_50.fastq
	~~6468 9033 BS_PE_DEL5_1000000_50_?~~.fastq		2355 4263 BS_SE_DEL5_1000000_50.fastq
	~~1743 10112 BS_PE_EXACT_1000000_50_?~~.fastq		441 4228 BS_SE_EXACT_1000000_50.fastq
	~~2305 231 BS_PE_INDEL30_1000000_50_?~~.fastq		809 764 BS_SE_INDEL30_1000000_50.fastq
	~~5703 2989 BS_PE_INDEL5_1000000_50_?~~.fastq		2217 3932 BS_SE_INDEL5_1000000_50.fastq
	~~1974 3718 BS_PE_SNP1_1000000_50_?~~.fastq		645 3808 BS_SE_SNP1_1000000_50.fastq
	~~2396 3339 BS_PE_SNP2_1000000_50_?~~.fastq		1102 3473 BS_SE_SNP2_1000000_50.fastq
	~~2817 3131 BS_PE_SNP3_1000000_50_?~~.fastq		1142 3267 BS_SE_SNP3_1000000_50.fastq
	~~4362 16074~~ CS_PE_DEL200_1000000_50_?.fastq		6193 6909 CS_PE_DEL200_1000000_50_?.fastq
	~~4385 -1~~ CS_PE_DEL30_1000000_50_?.fastq		6173 6636 CS_PE_DEL30_1000000_50_?.fastq
	~~4373 9287~~ CS_PE_DEL5_1000000_50_?.fastq		6096 6702 CS_PE_DEL5_1000000_50_?.fastq
	~~773 -1~~ CS_PE_EXACT_1000000_50_?.fastq		858 8496 CS_PE_EXACT_1000000_50_?.fastq
	~~1735 3142~~ CS_PE_INDEL30_1000000_50_?.fastq		1743 948 CS_PE_INDEL30_1000000_50_?.fastq
	~~4023 8591~~ CS_PE_INDEL5_1000000_50_?.fastq		5517 5412 CS_PE_INDEL5_1000000_50_?.fastq
	~~1034 10528~~ CS_PE_SNP1_1000000_50_?.fastq		1253 8454 CS_PE_SNP1_1000000_50_?.fastq
	~~2236 -1~~ CS_PE_SNP2_1000000_50_?.fastq		2113 7420 CS_PE_SNP2_1000000_50_?.fastq
	~~3810 6617~~ CS_PE_SNP3_1000000_50_?.fastq		2622 6076 CS_PE_SNP3_1000000_50_?.fastq
	~~7129~~ 1493 CS_SE_DEL200_1000000_50.fastq		3878 1493 CS_SE_DEL200_1000000_50.fastq
	~~7115~~ 1513 CS_SE_DEL30_1000000_50.fastq		3859 1513 CS_SE_DEL30_1000000_50.fastq
	~~7065~~ 1542 CS_SE_DEL5_1000000_50.fastq		3775 1542 CS_SE_DEL5_1000000_50.fastq
	~~1544~~ 1666 CS_SE_EXACT_1000000_50.fastq		621 1666 CS_SE_EXACT_1000000_50.fastq
	~~2954~~ 289 CS_SE_INDEL30_1000000_50.fastq		1392 289 CS_SE_INDEL30_1000000_50.fastq
	~~6547~~ 1390 CS_SE_INDEL5_1000000_50.fastq		3525 1390 CS_SE_INDEL5_1000000_50.fastq
	~~1690~~ 1661 CS_SE_SNP1_1000000_50.fastq		874 1661 CS_SE_SNP1_1000000_50.fastq
	~~2853~~ 1449 CS_SE_SNP2_1000000_50.fastq		1965 1449 CS_SE_SNP2_1000000_50.fastq
	~~4039~~ 1237 CS_SE_SNP3_1000000_50.fastq		3314 1237 CS_SE_SNP3_1000000_50.fastq
	</pre>		</pre>

Zhanxw: /* Available Test Datasets */

2010-02-11T19:52:30Z

Available Test Datasets

← Older revision		Revision as of 15:52, 11 February 2010
Line 47:		Line 47:

	Picked the 75 percentile of Sanger Iluumina 108 mer test data set		Picked the 75 percentile of Sanger Iluumina 108 mer test data set
			BCCCCBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBBAAAAAAAAAA@@@@@@@@@@@@@@@???????????>>>>>>>>>>>>=========<<<<<<<<<<;;";


	*Format		*Format

Zhanxw: /* Available Test Datasets */

2010-02-11T19:50:14Z

Available Test Datasets

← Older revision		Revision as of 15:50, 11 February 2010
Line 90:		Line 90:
	For illumina (from Sanger, 108mer hap1 test file):		For illumina (from Sanger, 108mer hap1 test file):
	Example:		Example:
			<pre>
	_1 file:		_1 file:
	@20:14812275:F:217;None;None/1		@20:14812275:F:217;None;None/1
Line 111:		Line 112:
	+		+
	%3===;==;7<<;7<5;==<<4<;9=8==<====:<<<<<;<==:=<58;===;:8'8:<===:.9:38908:=;;7;57)%.+%)967%%-%%'6:-%)7);<;0+%		%3===;==;7<<;7<5;==<<4<;9=8==<====:<<<<<;<==:=<58;===;:8'8:<===:.9:38908:=;;7;57)%.+%)967%%-%%'6:-%)7);<;0+%
			</pre>

	Conclusion:		Conclusion:
Line 120:		Line 122:
	For SOLiD (from Sanger, 50 mer hap1 test file)		For SOLiD (from Sanger, 50 mer hap1 test file)
	e.g.		e.g.

			<pre>
	_1 file:		_1 file:
	>2:67043752:F:1445;2,67043761,A,G;None		>2:67043752:F:1445;2,67043761,A,G;None
Line 134:		Line 138:
	>4:125830377:R:-1541;None;None		>4:125830377:R:-1541;None;None
	G13311131230200010201210032223330120312000301230032		G13311131230200010201210032223330120312000301230032

			</pre>

	Conclusion:		Conclusion:

Zhanxw: /* Available Test Datasets */

2010-02-11T19:49:15Z

Available Test Datasets

@@ Line 50: / Line 50: @@
 *Format
-both base space and color space both single end and paired end, and paired end reads are given insert size 1500.
+; Both base space and color space
 *Program (generator)
@@ Line 67: / Line 87: @@
 Simulation file are named like: BS_SE_EXACT_1000000_35, meaning base space, single end, exact (no polymorphism), 1M reads, 35 bp per read. For each read, the tag was named in a similar way to Sanger's.
-<br>
+* Example
 = Bulk statistics result  =

Zhanxw: /* Bulk statistics result */

2010-02-10T09:15:00Z

Bulk statistics result

← Older revision		Revision as of 05:15, 10 February 2010
Line 75:		Line 75:

	Log file is from runbatch.pl and negative time means unfinished (at the moment of editing).		Log file is from runbatch.pl and negative time means unfinished (at the moment of editing).

			TODO: Add file size comparison; add link to memory page summarized by Dharknes.
	<pre>		<pre>
	BWA(second) Karma(second) Scenarios		BWA(second) Karma(second) Scenarios

Zhanxw: /* Bulk statistics result */

2010-02-10T09:12:46Z

Bulk statistics result

← Older revision		Revision as of 05:12, 10 February 2010
Line 70:		Line 70:

	= Bulk statistics result =		= Bulk statistics result =
	Running time (all submitted to the MOSIX client ~~node~~)		Running time (all submitted to the MOSIX client nodes)
	<br>		<br>
			Calculated by "./parseRunbatch.py batch2.log \|cutrange 0,-1\|charrange :-1".

			Log file is from runbatch.pl and negative time means unfinished (at the moment of editing).
	<pre>		<pre>
	BWA(second) Karma(second) Scenarios		BWA(second) Karma(second) Scenarios

Zhanxw: /* Bulk statistics result */

2010-02-10T09:10:09Z

Bulk statistics result

← Older revision		Revision as of 05:10, 10 February 2010
Line 72:		Line 72:
	Running time (all submitted to the MOSIX client node)		Running time (all submitted to the MOSIX client node)
	<br>		<br>
			<pre>
	BWA(second) Karma(second) Scenarios		BWA(second) Karma(second) Scenarios
	2594 7182 BS_SE_DEL200_1000000_50.fastq		2594 7182 BS_SE_DEL200_1000000_50.fastq
Line 110:		Line 110:
	2853 1449 CS_SE_SNP2_1000000_50.fastq		2853 1449 CS_SE_SNP2_1000000_50.fastq
	4039 1237 CS_SE_SNP3_1000000_50.fastq		4039 1237 CS_SE_SNP3_1000000_50.fastq
			</pre>

Zhanxw at 09:09, 10 February 2010

2010-02-10T09:09:32Z

← Older revision		Revision as of 05:09, 10 February 2010
Line 70:		Line 70:

	= Bulk statistics result =		= Bulk statistics result =
			Running time (all submitted to the MOSIX client node)
	<br>		<br>