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| | == Mapping Qualities == | | == Mapping Qualities == |
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| − | We should evaluate mapping qualities by counting how many reads are assigned each mapping quality (or greater) and among those how many map correctly or incorrectly. This gives a Heng Li graph, where one plots number of correctly mapped reads vs. number of mismapped reads. | + | We should evaluate mapping qualities by counting how many reads are assigned each mapping quality (or greater) and among those how many map correctly or incorrectly. This gives a Heng Li graph, where one plots number of correctly mapped reads vs. number of mismapped reads. |
| − | | |
| − | == Available Test Datasets ==
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| − | | |
| − | *Location: wonderland:~zhanxw/BigSimulation
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| − | *Scenarios:
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| − | | |
| − | no polymorphism ; 1, 2, 3 SNP ; Deletion 5, 30, 200; Insertion 5, 30
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| − | | |
| − | *Quality String
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| − | | |
| − | Picked the 75 percentile of Sanger Iluumina 108 mer test data set
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| − | | |
| − | *Format
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| − | | |
| − | both base space and color space both single end and paired end, and paired end reads are given insert size 1500.
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| − | | |
| − | *Program (generator)
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| − | | |
| − | Usage:
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| − | | |
| − | generator [bs|cs] [se|pe] [exact|snpXX|indelXX|delXX] -n numbers -l readLength -i insertSize
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| − | exact: Accurate sample from reference genome
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| − | snpXX: Bring total XXX SNP for a single read or a pair of reads
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| − | indelXX: Insert a random XX-length piece for a single read, or at the same position for a paired reads
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| − | delXX: Delete a random XX-length piece for a single read, or at the same position for a paired reads
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| − | e.g. ./generator bs se exact -n 100 -l 35
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| − | | |
| − | *Output
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| − | | |
| − | 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.
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| − | | |
| − | <br>
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| − | | |
| − | = Bulk statistics result =
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| − | Running time (all submitted to the MOSIX client nodes)
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| − | <br>
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| − | Calculated by "./parseRunbatch.py batch2.log |cutrange 0,-1|charrange :-1".
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| − | | |
| − | Log file is from runbatch.pl and negative time means unfinished (at the moment of editing).
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| − | <pre>
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| − | BWA(second) Karma(second) Scenarios
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| − | 2594 7182 BS_SE_DEL200_1000000_50.fastq
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| − | 2641 -1 BS_SE_DEL30_1000000_50.fastq
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| − | 2355 -1 BS_SE_DEL5_1000000_50.fastq
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| − | 441 7941 BS_SE_EXACT_1000000_50.fastq
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| − | 809 282 BS_SE_INDEL30_1000000_50.fastq
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| − | 2217 -1 BS_SE_INDEL5_1000000_50.fastq
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| − | 645 7206 BS_SE_SNP1_1000000_50.fastq
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| − | 1102 -1 BS_SE_SNP2_1000000_50.fastq
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| − | 1142 -1 BS_SE_SNP3_1000000_50.fastq
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| − | 6536 8874 BS_PE_DEL200_1000000_50_?.fastq
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| − | 6699 9017 BS_PE_DEL30_1000000_50_?.fastq
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| − | 6468 9033 BS_PE_DEL5_1000000_50_?.fastq
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| − | 1743 10112 BS_PE_EXACT_1000000_50_?.fastq
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| − | 2305 231 BS_PE_INDEL30_1000000_50_?.fastq
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| − | 5703 2989 BS_PE_INDEL5_1000000_50_?.fastq
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| − | 1974 3718 BS_PE_SNP1_1000000_50_?.fastq
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| − | 2396 3339 BS_PE_SNP2_1000000_50_?.fastq
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| − | 2817 3131 BS_PE_SNP3_1000000_50_?.fastq
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| − | 4362 16074 CS_PE_DEL200_1000000_50_?.fastq
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| − | 4385 -1 CS_PE_DEL30_1000000_50_?.fastq
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| − | 4373 9287 CS_PE_DEL5_1000000_50_?.fastq
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| − | 773 -1 CS_PE_EXACT_1000000_50_?.fastq
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| − | 1735 3142 CS_PE_INDEL30_1000000_50_?.fastq
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| − | 4023 8591 CS_PE_INDEL5_1000000_50_?.fastq
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| − | 1034 10528 CS_PE_SNP1_1000000_50_?.fastq
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| − | 2236 -1 CS_PE_SNP2_1000000_50_?.fastq
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| − | 3810 6617 CS_PE_SNP3_1000000_50_?.fastq
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| − | 7129 1493 CS_SE_DEL200_1000000_50.fastq
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| − | 7115 1513 CS_SE_DEL30_1000000_50.fastq
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| − | 7065 1542 CS_SE_DEL5_1000000_50.fastq
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| − | 1544 1666 CS_SE_EXACT_1000000_50.fastq
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| − | 2954 289 CS_SE_INDEL30_1000000_50.fastq
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| − | 6547 1390 CS_SE_INDEL5_1000000_50.fastq
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| − | 1690 1661 CS_SE_SNP1_1000000_50.fastq
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| − | 2853 1449 CS_SE_SNP2_1000000_50.fastq
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| − | 4039 1237 CS_SE_SNP3_1000000_50.fastq
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| − | </pre>
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