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| *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 |
| | | |
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| | | |
| * Example | | * Example |
| + | |
| For illumina (from Sanger, 108mer hap1 test file): | | For illumina (from Sanger, 108mer hap1 test file): |
| + | |
| Example: | | Example: |
| <pre> | | <pre> |
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| | | |
| 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. |
| | | |