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Revision as of 15:49, 11 February 2010
, 15:49, 11 February 2010→Available Test Datasets
*Format
*Format
; 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
* Tag
@2:12345:F:SE:Exact
@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:Indel:25M30D5M
* File Naming
BS_SE_EXACT_1M_50
BS_SE_SNP1_1M_50
CS_SE_INDEL1_1M
CS_SE_INDEL30_1M
CS_SE_INDEL200_1M
CS_SE_DEL1_1M
For PE, appending "_1" and "_2", e.g.:
PE_EXACT_1M_1
PE_EXACT_1M_2
*Program (generator)
*Program (generator)
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.
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
For illumina (from Sanger, 108mer hap1 test file):
Example:
_1 file:
@20:14812275:F:217;None;None/1
AGTTGTTTACTTTCCTTTCCTACCTGGCTGCATCTGTCACATGCATATAGTGTCCCCTGACATGAAGCTCTGATATTGATCTGGAGCCCTATTGGTCTGCAAGTGACT
+
%27::2:::<70<<::95<<6/8<.)3;::9-,3:6/67731/.+)66;;53'31;9<815.%%%+%4-%%%90-)./26<831))(.%%%%%%%)%0%2%%%%%+%%
@15:59364621:R:-118;None;None/1
TGTTCAACCCACTATTAAGCCAGTATTAAATTGTTAATATCAGTTATTATACTTTTATTTCTAAAATTTCTATTTGATCCCTTTTTTTATAAACTCCAATGCATTCTC
+
%%2=;28>>>>=><>>>>>=>>=>>>;>=>9<1%+,//0+)<<91<4=;;<.%)2::8;;/9<;;;;8647<<;8;;066:<:4628;;;;5:9<<0/25752:3482
_2 file:
@20:14812275:F:217;None;None/2
CACTGGAGGGAATCCAATCCCAAATTAATATAACAAAACCAGAAGCTTGCTTAAAAAATATTTTATCAGATTCCAAAGTTGAGCTTGTGTTAGGGTGTACTGGAACTC
+
%%0;+250::-863486::599<9679/2%%))%+80%--7<;9/1%33,-%%)28/),3,67-8;56<1%)0/%%8;<;59/%%,())%%1%%+%).%099'4;+%-
@15:59364621:R:-118;None;None/2
AGAAATAAGACCACATGACAATGTTAAAAATAAAACAGGCAATAGCAATAGTCCCAGAGGTGGTTACAATATGATTTCATGCTCCAGAAAGTATAGGAGAAGACAAAG
+
%3===;==;7<<;7<5;==<<4<;9=8==<====:<<<<<;<==:=<58;===;:8'8:<===:.9:38908:=;;7;57)%.+%)967%%-%%'6:-%)7);<;0+%
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 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 second strand position is first strand position plus the offset.
For SOLiD (from Sanger, 50 mer hap1 test file)
e.g.
_1 file:
>2:67043752:F:1445;2,67043761,A,G;None
T12221203021201200302123102221322000012301300211213
22212031230012003021211022213220000123013022112123 (ref)
>4:125830377:R:-1541;None;None
T30002222300330113020203010322111010300030003230320
_2 file:
>2:67043752:F:1445;2,67043761,A,G;None
G13031223023023012201210020003310110111111203310211
30312230230230122012100200033121201111113033112112 (ref)
>4:125830377:R:-1541;None;None
G13311131230200010201210032223330120312000301230032
Conclusion:
The first strand and second strand have the same direction (both either same as the reference genome, or reverse complement to reference genome),
where their positions are the same as Illumina reads.
<br>
= Bulk statistics result =
= Bulk statistics result =
