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Jump to navigationJump to searchEvaluating a Read Mapper on Simulated Data (view source)
Revision as of 20:12, 16 February 2010
, 20:12, 16 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
* 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
* Example
* Example
For illumina (from Sanger, 108mer hap1 test file):
For illumina (from Sanger, 108mer hap1 test file):
Example:
Example:
<pre>
<pre>
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.
